I have an electric fan forced air heater at 2000 watts powered by 240 volt wiring, hot/hot. I have a 12/2 wire that comes from power and connects to it, it works great and no problem. I want to add a 5/2 programmable in line thermostat. Is there a way to do that, without running power to the thermostat first, then running it to the heater, again, this is an inline 240 volt rated thermostat from Honeywell, and the supply already goes to the heater itself. I don't want to (if possible) have to rewire it so it goes to the thermostat first, but rather have it run to it second, i.e.. Put the thermostat at the endo fot he line. I tried to do this, and it powers fine, but is still controlled by the onboard thermostat switch on the heater. So I am doing something wrong. Can anyone help? Thanks!

In ANY case the thermostat has to be (electrically) ahead of the heat that it controls. You will need a 12-2 from the panel to the tstat and another 12-2 back to the heat.

Assuming there is enough room to junction all those wires inside the wireing cavity of your heater, you could run two 12-2 cables from the heater to the thermostat. The first one would connect to the line from the electric panel with NO connection to any part of the heat except for the grounding (bare or green) conductor. The other end of that first cable would go to the input or LINE terminals of the thermostat. The second 12-2 would come back from the LOAD terminals of the thermostat and would connect to the heat strip. Most likely you would eliminate the existing thermostat mounted in the heating unit.