I have both the cb70 and the sweaterbox racks for reptile basic. they are both ran using different temp probes. yes the herpstat 2 has 2 probes and 2 slots for the powercord coming off of the flexwatt. and will work for your setup. you will just need to get another thermostat when you build your incubator.
I'm actually building my incubator this weekend, so I'll run it off the herpstat. I'm also going to run the sweaterbox off the herpstat. The CB-70 rack I'll run off a hydrafarm that I've got laying around until I can purchase another.