You could always get a herpstat 2, I believe that allows you to control seprately 2 different temperature areas. That would be easier and I think cheaper than buying two regular herpstats or helixes.

As far as wiring goes if you wire up each strip of flexwatt individually and run them to a power strip which could be plugged into the thermostat. Just each individual temperature area would need its own power strip. That's how I have my corn rack set up and it works great.