Well, it's not complicated. I even provided presets for A1200, A500 and Workbench usage in the archive, in Conf/ directory.
Assuming you put the kickstart files in the right place (roms/ directory), you just start UAE that way:

uae -f conf/A500.conf or
uae -f conf/A1200.conf or
uae -f conf/wb.conf
and so on ...

if you need to pass an adf, you do it that way:
uae -f conf/A1200.conf -0 blah.adf

Now, i suggest you bind UAE to ADF mimetype in Ambient with that kind of commaand : path:to/uae/uae -f path:to/uae/conf/blah.conf -0 %sp to ADF
That way, you can start any ADF just by doubleclicking it.

[ Edited by Fab 14.06.2012 - 08:33 ]

@Fab

Thanks for the answer

I will try this out when I come home from my wakation.
Sorry for sounding so negative, it is probably not so hard to set up
wen Im not so stresed.