You'll have no problem installing FMS alongside IIS (any flavor). FMS/FCS and
your http server are independant from each other, so it really doesn't matter
which http server you use.

Keep in mind that if you want to use FMS's tunneling capabilities, you'll need
to have a separate IP for FMS. Tunneling (by default) runs on port 80, which is
the default port for http traffic. If you have both your webserver and FCS
listening to port 80 on the same IP, one of them will fail to receive incoming
traffic.

I have a tutorial here that may help you:
http://www.flashcomguru.com/tutorials/fcs_iis.cfm

stoem