The readme says "documentation is a work-in-progress, please see Docs directory". One problem, there is no Docs directory. Google is not as helpful as I'd like.
I got EUAE working, but I would like to tweak it. Hard to tweak settings without docs.
There shouldn't be any difference to the original uae options, except for the addition of overlay output, that is done with amiga.use_overlay= true|false.
And you can forget about network bsd emulation and JIT at least. The options will be accepted, but that's it. :)