Well It depends on what you mean
1 If you mean you wanna rearrange the menu's it done like
v3 - Edit Index.php and move the code about or add new code (just copy and paste another and edit)
v3.5 - In includes/xml/cpnav_vbulletin.xml and rearrange them in there or add new code (same as above)
2. If you mean adding actual frames then it's editing index.php for all versions
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