I have the navbar in the top frame of a frameset, but when the menus open they disappear behind the border. How do I fix that?
You can't. The pages of a frameset are discreet - frames are top-level objects like windows - so content from one frame cannot hang over the lip into another.
There is a fundamental problem with framesets, and I strongly discourage anyone from using them. If you use this menu you have no need for a navigation frame; simply put the script includes on each page, and any changes you make to custom.js will be reflected throughout. Furthermore, the menu scripts are always cached after their first use, even on html pages which don't cache themselves.
However if you insist ... it is possible to script a topnav in one frame and then send the menu-building or show/hide commands to another frame. There are scripts at Dynamic Drive which can do that.