The file user-startup (System/S/user-startup) is a text file and can be edited in a text editor. You can edit this file from the host computer (i.e. Mac OS X in your case).
But these questions are now getting very Amiga-specific and very much less about FS-UAE. I recommend you create a user account at the English Amiga Board forums. There are many Amiga enthusiasts there, and some may have experience with this software (which I don’t have), so if you create a thread there asking for help with this software, I’, sure you’ll get better answers. There’s a sub-forum called support.Apps which should be suitable. There’s also support.FS-UAE for FS-UAE-related discussion and help.