I was able to get things to work by using the Mage tool as described here:
http://msdn.microsoft.com/en-us/library/6fehc36e.aspx
The trick with MageUI is it's open file dialog assumes you want to open a manifest associated with a .exe; a vsto project has a .dll, so the manifest doesn't appear in the files list by default, which was really tripping me up.
Basically, this process is a pain because you have to remember to do it manually. I don't know if there's a way to make this part of the build (maybe a post-build step? But this is really a post-publish step).