My bookmark.nsf launches the "Main Frameset" frameset. From what I've read it looks like a policy pushes the custom bookmark.nsf down onto the user's PC.

 

It sounds like you need to replace the "Main Frameset" design element in each user's Bookmark.nsf with your new one. If you want to use a different frameset, the default frameset to launch is stored in the Icon design element ($DefaultFrameset field)

The "home" database is a flag (of sorts) in the UserBookmarkOrder outline, but it's not accessible via LotusScript or the published Notes API as far as I know. The way you set it in Domino Designer is to use a weird Shift-click combination on the outline entry:

 

http://www-01.ibm.com/support/docview.wss?rs=475&uid=swg27003219

 

Interestingly enough though, I think that if you copy an outline entry with that special flag set, it will retain the flag when it's pasted. You might want to play around with that. Other clues here: 

 

http://www-10.lotus.com/ldd/46dom.nsf/ReleaseAllThreadedweb/b50cb5690c89707b85256baa0055c018?OpenDocument