Really, the only way to do this functionally is with virtualization of the host(s). Or running them on separate boxes.

Consider a request to the two different servers. Assume two different IP addresses on different subnets, different DNS domains, and different DNS servers providing those zones. Even consider the machine they're being hosted on being multi-homed, with two different paths to the IP addresses for each site.

If they're still running on the same apache process on the same box, you can tell.

Fire up your favorite stress tester and point it at one of the sites, and start hitting it hard - and the other one will likely slow down.

It's possible that if you ran one apache process on one port, and and entirely separate one on another port, and you tuned the heck out of them, this sort of evidence might be hard to discover. But really, eventually, someone would be able to tell.

Now, if you're asking how to just keep them separate functionally, different IPs and different DNS along with a decent apache virtual configuration will provide that. Of course, if you bring down one (i.e. apache is restarted or stopped) you will bring down the other one as well. So, if you need that sort of separation, look at virtualization, or run them on different hosts.