Add support for themes
In overlay_theme\app or overlay_theme\framework create directory with apk
name and place there your changed files.
It should look like:
overlay_theme\app\SystemUI.apk\res\layout\carrier_label.xml
or:
overlay_theme\framework\framework-res.apk\res\drawable-nodpi\tw_background_holo_dark.png

If Kitchen will detect, that any apps from theme directory don't exist in
current ROM, they'll be automatically listed in overlay_theme\THESE_APPS_DONT_EXIST.txt
or THESE_FRAMEWORKS_DONT_EXIST.txt