A little progress - there is very little, if any, documentation on using fs-uae in RetroPie.
I tried running a few games and kept getting a message that it wanted kick1.3.rom, so I renamed the kickstart 13. rom kick1.3.rom and then I would get a kickstart 1.3 splash screen but no more progress. I tried a few more games and finally Lemmings seemed to load, however this gets stuck at the Load Disc 2 screen?
So this is probably a configuration / path problem however I don't know how to resolve it?