... direct from the the linux desktop using eau and different config files?
Do you mean UAE? or E-UAE? I have never heared of a program called eau. (Would be a nice name though.)
I´d assume you´d simply create a uaerc for every adf you want to start and make a bash script to run uae with it. Depending on your desktop environment, you might do something to make the script clickable.
Was this what you were thinking of? RTFM:
man uaeEDIT Oh, wait! aparently UAE prefers you go with one single .uaerc in your $HOME.
uae -s floppy0=/usr/home/haywirepc/adfs/dpaintiv.adf
should do the trick.
