Following this got my project set up exactly the way I wanted it and allows me to update the copy of the main project whenever I want to: http://debuggable.com/posts/git-fake-submodules:4b563ee4-f3cc-4061-967e-0e48cbdd56cb
If anyone else wants to use this but runs into problems with pulling new versions of the base project, stash your changes before you pull.