I have a .emacs.d directory shared (via git) with branches for various projects and Aquamacs seems to be ignoring it completely. All the other development systems work very well with this system so I would prefer to keep it if it can be made to work with Aquamacs.
Aquamacs uses it's own series or .emacs like files, one is called Preferences.el (this is the aquamacs equivlent of .emacs) and it's located at ~/Library/Applications Support/Aquaemacs/. Personally, I didn't like aquaemacs, and switched to Carbon emacs on OS X. All this info is in the aquamacs documentation.