When running ColdFusion 9 in multiple instances, you used to be able to run the Web Server Connector tool from the Windows start menu and connect specific instances to sites. This changed in ColdFusion 10.
The Web Server Connector tool in the Windows start menu for ColdFusion 10 will only allow you to connect websites to the CFUSION (main) instance. If you want to connect a site to a different instance, you'll need to run the connector tool just for that instance.
For example, if you have an instance named “www”, you need to go to the following executable to connect an IIS site to the “www” instance.
<cf install root>\www\runtime\bin\wsconfig.exe
The www in bold is the instance name.
I'm sure this is somewhere in the install documentation, but I missed it and lost a bunch of time trying to figure out how to get sites to run off of different instances.