Q:

Where do I specify the file path for phtml? ( Clarification please)

Where do I put the phtml file that all of this works with? 
Current Files and their folder structure:
app/code/local/Sean/Customform/controllers/IndexController.php
<? php
class Sean_Customform_IndexController extends Mage_Core_Controller_Front_Action{
    public function indexAction(){ //this will display the form
        $this->loadLayout();
        $this->_initLayoutMessages('core/session'); //this will allow flash messages
        $this->renderLayout();
    }
    public function sendAction(){ //handles the form submit
        $customer = Mage::getSingleton('customer/session')->getCustomer();
        $post = Mage::app()->getRequest()->getParams();

        $customer->setData('vendorMarkup', $post['vendorMarkup']);
        $customer->setData('vendorGramPrice', $post['vendorGramPrice']);
        $customer->setData('vendorGramFront', $post['vendorGramFront']);
        $customer->setData('vendorGramBack', $post['vendorGramBack']);
        $customer->setData('vendorDefaultCalc', $post['defaultMarkup']);
        $customer->save();

        Mage::getSingleton('core/session')->addSuccess($this->__('Your Calculator Preferences Are Updated!'));//add success message. 
        $this->_redirect('*/*');
    }
}

app/code/local/Sean/Customform/etc/config.xml
<? xml version="1.0"? >
<config>
    <modules>
        <Sean_Customform>
            <version>0.0.1</version>
        </Sean_Customform>
    </modules>
    <global>
        <blocks>
            <customform><!-- block alias -->
                <class>Sean_Customform_Block</class>
            </customform>
        </blocks>
        <helpers>
            <customform><!-- helper alias -->
                <class>Sean_Customform_Helper</class>
            </customform>
        </helpers>
    </global>
    <frontend>
        <routers>
            <customform>
                <use>standard</use>
                <args>
                    <module>Sean_Customform</module>
                    <frontName>customform</frontName><!-- url key for module -->
                </args>
            </customform>
        </routers>
        <layout>
            <updates>
                <sean_customform>
                    <file>sean_customform.xml</file><!-- frontend layout file -->
                </sean_customform>
            </updates>
        </layout>
        <translate>
            <modules>
                <Sean_Customform>
                    <files>
                        <default>Sean_Customform.csv</default><!-- translation file (not mandatory) -->
                    </files>
                </Sean_Customform>
            </modules>
        </translate>
    </frontend>
</config>

app/code/local/Sean/Customform/helper. Data.php
<? php
class Sean_Customform_Helper_Data extends Mage_Core_Helper_Abstract{
}

And of course, app/etc/modules/Sean_Customform.xml
<? xml version="1.0"? >
<config>
    <modules>
        <Sean_Customform>
            <active>true</active>
            <codePool>local</codePool>
        </Sean_Customform>
    </modules>
</config>

A:

In your config.xml file, you have this part. 
    <layout>
        <updates>
            <sean_customform>
                <file>sean_customform.xml</file><!-- frontend layout file -->
            </sean_customform>
        </updates>
    </layout>

This defines a frontend layout xml file sean_customform.xml which is going to hold all frontend layout definition specifically for your module.  You can find this file at location app/design/frontend/base/default/sean_customform.xml. 
Here you will find your form.phtml file inclusion.  
So basically you have a dedicated layout xml for your module and all module related layout definition is going to happen in that layout xml file (in this case, it is sean_customform.xml).  This file will hold all phtml files.