Check out my blog post on this.
Flex-Data-Server-and-CF-Flash-Remoting-togetherJust install the 2 products, as 2 servers and start them up,
they can find each other automatically. Granted you have more
control if you use the multi-server mode (you can deploy them as 2
.war file applications in one server ). But as long as both servers
are running you should be all set.
The only time you need to merge the servers, is if you want
to serve both .mxml and .cfm files from your web server. However
it's a much better idea to pre-compile the movies and just server
the compiled .swf (like you would for any other flash
movie).