[Galaxy S II General] Namoi:
Hmm, if i remember correctly when i did this (long time ago) i had problem with the notification too as some of them get under the toggles. I fixed it by adding a android:layout_marginBottom="90.0dip" ro bring the notification drawer up. The dip depend of your layout.

Here is my code (forget the com.android.systemui on yours it should remains systemui). In red the margin.

<?xml version="1.0" encoding="utf-8"?>
<FrameLayout android:id="@com.android.systemui:id/notification_panel" android:background="@com.android.systemui:drawable/notification_panel_bg" android:layout_gravity="top" android:paddingTop="25.0dip" android:layout_width="match_parent" android:layout_height="match_parent" android:layout_marginLeft="@com.android.systemui:dimen/notification_panel_margin_left"
xmlns:android="http://schemas.android.com/apk/res/android"
xmlns:systemui="http://schemas.android.com/apk/res/com.android.systemui">
<FrameLayout android:layout_width="fill_parent" android:layout_height="fill_parent" android:layout_marginBottom="@com.android.systemui:dimen/tw_close_handle_underlap">
<include android:layout_width="fill_parent" android:layout_height="@com.android.systemui:dimen/tw_notification_panel_header_height" layout="@com.android.systemui:layout/tw_status_bar_expanded_header" />
<TextView android:gravity="center" android:id="@com.android.systemui:id/emergency_calls_only" android:paddingBottom="4.0dip" android:visibility="gone" android:layout_width="fill_parent" android:layout_height="wrap_content" />
<View android:background="#ff091a24" android:layout_width="fill_parent" android:layout_height="1.0dip" android:layout_marginTop="@com.android.systemui:dimen/tw_notification_panel_header_height" />
<ScrollView android:id="@com.android.systemui:id/scroll" android:fadingEdge="none" android:layout_width="fill_parent" android:layout_height="fill_parent" [COLOR=Red][COLOR=Black]android:layout_marginBottom="44.0dip"[/COLOR] [/COLOR]android:layout_marginTop="@com.android.systemui:dimen/tw_notification_panel_header_line_height" android:overScrollMode="ifContentScrolls">
<LinearLayout android:orientation="vertical" android:id="@com.android.systemui:id/scrollCart" android:layout_width="fill_parent" android:layout_height="wrap_content" android:divider="@*android:color/transparent">
<HorizontalScrollView android:id="@com.android.systemui:id/quicksetting_scroller" android:scrollbars="none" android:layout_width="0.0dip" android:layout_height="0.0dip">
<com.android.systemui.statusbar.policy.quicksetting.QuickSettingPanel android:orientation="horizontal" android:id="@com.android.systemui:id/quicksetting_container" android:visibility="gone" android:layout_width="wrap_content" android:layout_height="wrap_content" android:divider="@com.android.systemui:drawable/tw_black_bg" android:showDividers="middle" />
</HorizontalScrollView>
<LinearLayout android:orientation="vertical" android:id="@com.android.systemui:id/brightness_controller" android:background="#00000000" android:layout_width="fill_parent" android:layout_height="56.0dip">
<View android:background="#ff091a24" android:layout_width="fill_parent" android:layout_height="1.0dip" />
<LinearLayout android:orientation="horizontal" android:layout_width="fill_parent" android:layout_height="55.0dip">
<ImageView android:id="@com.android.systemui:id/brightness_icon" android:clickable="true" android:layout_width="25.0dip" android:layout_height="fill_parent" android:layout_marginLeft="13.0dip" android:src="@com.android.systemui:drawable/ic_sysbar_brightness" android:contentDescription="@com.android.systemui:string/accessibility_brightness_icon" />
<FrameLayout android:id="@com.android.systemui:id/brightness_group" android:layout_width="fill_parent" android:layout_height="fill_parent">
<com.android.systemui.statusbar.policy.ToggleSlider android:id="@com.android.systemui:id/brightness" android:layout_width="fill_parent" android:layout_height="fill_parent" systemui:text="@com.android.systemui:string/status_bar_settings_auto_brightness_label" />
<com.android.systemui.statusbar.policy.ToggleSlider android:id="@com.android.systemui:id/auto_brightness" android:layout_width="fill_parent" android:layout_height="fill_parent" systemui:text="@com.android.systemui:string/status_bar_settings_auto_brightness_label" />
</FrameLayout>
</LinearLayout>
<View android:background="#ff091a24" android:layout_width="fill_parent" android:layout_height="0.0dip" />
</LinearLayout>
<LinearLayout android:orientation="vertical" android:id="@com.android.systemui:id/noNotificationsTitle" android:focusable="true" android:layout_width="fill_parent" android:layout_height="0.0dip">
<TextView android:textSize="@com.android.systemui:dimen/status_bar_expanded_notification_category_text_size" android:textColor="@com.android.systemui:color/notification_category_color" android:gravity="left|center" android:id="@com.android.systemui:id/noNotificationsText" android:paddingLeft="11.0dip" android:layout_width="fill_parent" android:layout_height="@com.android.systemui:dimen/status_bar_expanded_notification_category_height" android:text="@com.android.systemui:string/status_bar_no_notifications_title" />
</LinearLayout>
<LinearLayout android:orientation="vertical" android:id="@com.android.systemui:id/onGoingCart" android:background="#ff293945" android:focusable="true" android:visibility="gone" android:layout_width="fill_parent" android:layout_height="0.0dip">
<TextView android:textSize="@com.android.systemui:dimen/status_bar_expanded_notification_category_text_size" android:textColor="@com.android.systemui:color/notification_category_color" android:gravity="left|center" android:id="@com.android.systemui:id/onGoingNotificationText" android:paddingLeft="11.0dip" android:layout_width="fill_parent" android:layout_height="fill_parent" android:text="@com.android.systemui:string/status_bar_ongoing_events_title" />
</LinearLayout>
<com.android.systemui.statusbar.policy.NotificationRowLayout android:id="@com.android.systemui:id/onGoingItems" android:layout_width="fill_parent" android:layout_height="wrap_content" systemui:rowHeight="@com.android.systemui:dimen/tw_notification_row_min_height" />
<LinearLayout android:orientation="vertical" android:id="@com.android.systemui:id/notificationCart" android:background="#ff293945" android:visibility="gone" android:layout_width="fill_parent" android:layout_height="0.0dip">
<RelativeLayout android:orientation="horizontal" android:layout_width="fill_parent" android:layout_height="wrap_content">
<TextView android:textSize="@com.android.systemui:dimen/status_bar_expanded_notification_category_text_size" android:textColor="@com.android.systemui:color/notification_category_color" android:gravity="left|center" android:id="@com.android.systemui:id/latestNotificationText" android:paddingLeft="11.0dip" android:layout_width="180.0dip" android:layout_height="fill_parent" android:text="@com.android.systemui:string/status_bar_latest_events_title" android:layout_alignParentLeft="true" />
<TextView android:textSize="@com.android.systemui:dimen/status_bar_expanded_notification_clear_button_text_size" android:textColor="@com.android.systemui:color/tw_status_bar_clear_btn_text" android:gravity="center" android:id="@com.android.systemui:id/clear_all_button" android:background="@com.android.systemui:drawable/tw_btn_default_small" android:padding="0.100000024dip" android:focusable="true" android:clickable="true" android:layout_width="@com.android.systemui:dimen/status_bar_expanded_clear_button_width" android:layout_height="fill_parent" android:layout_marginRight="4.0dip" android:text="@com.android.systemui:string/status_bar_clear_all_button" android:layout_alignParentRight="true" android:contentDescription="@com.android.systemui:string/accessibility_clear_all" />
</RelativeLayout>
</LinearLayout>
<com.android.systemui.statusbar.policy.NotificationRowLayout android:id="@com.android.systemui:id/notificationItems" android:layout_width="fill_parent" android:layout_height="wrap_content" systemui:rowHeight="@com.android.systemui:dimen/tw_notification_row_min_height" />
<com.android.systemui.statusbar.policy.NotificationRowLayout android:id="@com.android.systemui:id/latestItems" android:layout_width="fill_parent" android:layout_height="wrap_content" systemui:rowHeight="@com.android.systemui:dimen/tw_notification_row_min_height" />
</LinearLayout>
</ScrollView>
</FrameLayout>

<View android:background="#ff091a24" android:layout_width="fill_parent" android:layout_height="1.0dip" android:layout_gravity="bottom" [COLOR=Red]android:layout_marginBottom="90.dip"[/COLOR]/>

<HorizontalScrollView android:scrollbars="none" android:layout_width="match_parent" android:layout_height="55.0dip" android:layout_marginBottom="35.0dip" android:layout_gravity="bottom">
<com.wanam.systemui.quickpanel.PowerWidget android:id="@com.android.systemui:id/exp_power_stat" android:layout_width="wrap_content" android:layout_height="55.0dip" />
</HorizontalScrollView>

<View android:background="#ff091a24" android:layout_width="fill_parent" android:layout_height="1.0dip" android:layout_gravity="bottom" android:layout_marginBottom="@com.android.systemui:dimen/tw_close_handle_height"/>

<com.android.systemui.statusbar.phone.CloseDragHandle android:layout_gravity="bottom" android:orientation="vertical" android:id="@com.android.systemui:id/close" android:layout_width="fill_parent" android:layout_height="@com.android.systemui:dimen/tw_close_handle_height">
<RelativeLayout android:layout_width="fill_parent" android:layout_height="fill_parent">
<ImageView android:layout_gravity="bottom" android:layout_width="fill_parent" android:layout_height="@com.android.systemui:dimen/tw_close_handle_height" android:src="@com.android.systemui:drawable/tw_status_bar_close" android:scaleType="center" />
<TextView android:textAppearance="@com.android.systemui:style/TextAppearance.StatusBar.Expanded.Network" android:gravity="center" android:layout_gravity="bottom" android:id="@com.android.systemui:id/carrier_label" android:textSize="0.0dip" android:layout_width="fill_parent" android:layout_height="@com.android.systemui:dimen/tw_close_handle_height" android:layout_marginBottom="18.0dip" />
</RelativeLayout>
</com.android.systemui.statusbar.phone.CloseDragHandle>

</FrameLayout>

And a screenshot of the result.

EDIT : i hope it's this margin, but TBH i don't remember exactly.