It shouldn't be that hard to get them both going under one thermostat. The only issue would be if one system is blowing more heat then the other and that side ends up being warmer because of the thermostat placement. At least with two you could turn one down.
As it is now, one side is off and one side is on. I'm willing to adjust the one thermostat up or down to get a desired temp, if we can get a pretty consistent heat on both sides.
