This is actually pretty basic, but I had a hard time with it this morning, so I thought I'd share how to do this.
I created a host and host instance on our BizTalk server specifically to host the receive locations we are running. Creating the host and instance was no problem, but I had a hard time changing the receive locations to use the new host. In the BizTalk Administration Console as well as in BizTalk Explorer, there is a place to choose the Receive Handler - the problem was that this dropdown contained only the original host, not the new one.
It turns out that the host is associated with the receive adapter, not each instance. So the solution is to go to the Adapters node in the BizTalk Administration Console, choose the Adapter, choose Receive Locations, and then specify the host. This changes it for all receive locations using that host. It's actually documented here, so I'm not sure why I had so much trouble finding the answer.