What do you need IIS for? Are you intending to use IWP, or the PHP API or XML publishing?
FileMaker Server should be able to use IIS alongside other webpages (IWP uses a virtual folder within the default website, and takes to default URL http://yourserver.web/fmi/iwp/ )
That said, I have sometime experienced some difficulties deploying IWP when another application is also trying to use IIS, but not when IIS was just hosting simple webpages.
If you have the resources, you can certainly deploy FileMaker server as a two-server solution (one server hosting the databases, the other hosting the web services, such as IWP). That's one of the standard options when installing FileMaker server, when you are asked about web-deployment. Just run the FileMaker Server deployment wizard.
Hope this helps,
I had missed out on the deployment options.
My FileMaker server is also a Windows Essentials server, so there are Web apps in the Default Web site.
I have everything setup on a another machine now.