If you want to individually monitor instances of websites on different servers, then one approach would be to install an DNS server in your network, and resolve the host to the IP addresses yourself.
You would want to set a low TTL on each A record to make sure that each resolution resulted in a different IP address.
For example:
www.domain.com. 10 A 111.111.111.111 www.domain.com. 10 A 111.111.111.112 This assumes that you have a single website served by the two IP addresses on the end.
The 10 value is the TTL and tells the client how long the record is valid for before it should query the server again. As there are two possible IP addresses, the DNS server will "round-robin" and serve them one at a time. So if your polling was every 10 seconds, this would alternate between the two IP addresses.