At risk of answering my own question, I thought I'd share my findings in case anyone else has the same issues.
For the Amiga performance issue, I created a config file called Default.fs-uae in /user data/system/configs/FS-UAE/Configurations
I then added the following lines to it:
accuracy = 0
By doing this, the Amiga 500 emulator so far runs fine. I understand that it might impact compatibility with some software, but so far so good.
For the C64 vice emulator I noticed it ran fine if I disabled the sound from the f12 menu, so I edited the /user data/system/configs/vice/vice.conf file to set SidEngine=0 and SidModel=0
I'm assuming that turns off a more advanced Sid emulator as I now can have sound and run C64 games and they work fine.
Also, finally on the vice emulator, you can speed up the loading of games by hitting alt w for warp mode, then hit it again when the game starts to run. They're still not massively fast, but better.
So there you go, hope that is vaguely useful to someone. Also, if anyone has better ideas how to improve performance please let me know!