Are you using regular UAE or EUAE? If you're not using
EUAE I'd suggest you use it instead since it contains some code borrowed from WinUAE such as the JIT compiler and so on.
BTW I'm not sure how great the GUI is on it but it has one and I have used it before. It will use hardfiles but you may have to edit ~/.uaerc by hand. I don't know how to create a new hardfile on Linux since I just copied my hardfile from my Windows partition.
