I am used to using WinUAE.
Using E-Uae on MorphOS sucks because you have to use Shell to launch it.
Is there a nice GUI or frontend for it?
First, which E-UAE archive did you use?
If you got mine, there's at least an explanation and default config files for A500 and A1200, "workbench" usage, and so on.
So, if you use them, just have kick.rom (A1200 3.x) and kick13.rom (A500 1.3) in the Roms/ directory, and from shell, you can type (from UAE directory):
e-uae -f conf/A1200.conf -0somedisk.adf -1someotherdisk.adf
If you need to configure things, have a look at the different config files in conf/.
Finally, you can bind UAE to Ambient with its mimetypes, which means you can start any adf by simply doubleclicking it. But we'll see that when you at least get UAE to work.