Install user-specific preferences and packages in the paths within the user’s home folder (~), system-wide preferences go in /Library/...

Install Aquamacs-specific preferences and packages in Aquamacs Emacs paths, others (which should be loaded by other Carbon Emacsen) in Emacs paths.

Preferences (.emacs)

These preferences are loaded, in the given order:

 ~/.emacs  (deprecated -- meaning 'should not be used for new installations, but will continue to be supported' -- in Aquamacs on OS X)
 customizations saved by request or automatically by Aquamacs in customizations.el
 /Library/Preferences/Aquamacs Emacs/Preferences.el
 ~/Library/Preferences/Aquamacs Emacs/Preferences.el

Manual user-specific customizations should go into ~/Library/Preferences/Aquamacs Emacs/Preferences.el

Note that code in Preferences.el (but not .emacs) will override any settings in customizations saved by Aquamacs (Options / Save Options, and saving at the end of a session when quitting Aquamacs).

Warning: this is not the page to describe miscellaneous extensions to Aquamacs. Go to CustomizeAquamacs for that.