I thought that I read a thread discussing this exact problem but I can't find it (try looking for it).
I'm not sure if this answers your question, but the following discusses how to use an existing installation of Apache HTTP Server other than the one that installs with Flash Media Server:
http://help.adobe.com/en_US/flashmediaserver/configadmin/WSd391de4d9c7bd6093a7e2f8312a374a1bde-8000.html#WS565cbb3ff5441e2614fa39ef13121395a10-8000
The topics are somewhat similar so the steps suggested by the article might point you in the right direction.
> I installed FMS 4.5 and unticked the Apache install option so there would be no conflicts.
Note that the article instructs you to install Apache as part of FMS in order to copy the Apache files to the other server. You might have to re-intall FMS with Apache server selected, follow the instructions above, then uninstall the Apache server that you will not be using.
Good luck.