I did not get your requirement clearly but let me try to answer it.
First of all there is no issue of having web server and FMS on same machine , only thing it might fight for resources in case of high traffic, but there is no issue per se of having them on same machine.
Second thing, I do not know whether you are aware of it or not, but FMS comes with in-built Apache Web server so you can decide to use it if you want and host your client applications there.
Third thing, i did not get what did you mean by "I'm assuming it's just like the developer version where it can run on localhost, correct? " - Are you saying you can hardcode you URI to localhost - if you are under that impression, please let me correct you. You URI should point to domain name or IP address of FMS (in this case same as your webserver) because your client swf would get downloaded to client's browser and "localhost" in that case would point to "client's machine" and not your FMS/Webserver.
let me know if you still have open questions.