Hiya, the ~/.uaerc file can be generated automatically using the config GUI. If when you start E-UAE you do not get a configuration dialog, run ./configure --help in the source code directory and examine the arguments to configure the GUI. Being at work, I don't have a source tree handy to tell you explicitly what to configure ;-) In my experience it is automatically enabled if you have GTK2 dev packages installed on your machine.
The config dialog should be fairly easy to drive, let us know if you have issues with it! You need to hit "save" to generate the ~/.uaerc file.