The same story in Linux really. Emulators in general are pretty poor there, and the whole Linux 'backend/frontend' method just doesn't work for me.
WinUAE with it's integrated GUI and unbelievable feature set won't be beaten.
I think Fred has the right idea. There's no point struggling with rubbish emulators (with all due respect to the developers) when you can install Windows and use it solely for that.