In this current BCC release, you might want to install it on the both the boxes
and have two web sites and I hope its not much of an inconvenience.
NOTE: If you have clustered BizTalk boxes, I guess then both the host instances would show up on one box. In that case you can install BCC on just the primary server.
Some points to note:
1. When you enable monitoring on both the boxes, you would get an email notification on which box the failure has happened. So that will tell you which box to look into.
2. The upcoming 4.0 release will address the multi-server scenario.