It depends on how the servers are binding to the same port.
The options I could see are:
1. The host is binding on different IP addresses
If this is the case, you should be able to setup an input for each IP address.
2. The web-servers are behind a reverse proxy and are using domain names to distinguish between both of them
In this case, you should be able to setup an input for each host name to has the inputs distinguish between each server. The app supports SNI and thus should work even if the sites use SSL.
3. The web-servers are behind a reverse proxy that is load-balancing
In this case, it may not be possible to have separate inputs that monitor both of the sites or to guarantee when both sites would be monitored (unless the reverse proxy has some way of allowing you specify which server to go to).