Yes you can run the heater with the thermostat, but there are some things to consider. You will need to know what the wattage handling capability of the thermostat is. On my oil filled heater there is a 3 positioned switch marked I-II-III, which amounts to Low-Med-High. This switch determines how fast the heater will heat up by using different wattages. For my heater, Low= 300 Watts, Med= 600 Watts, and High= 1500 Watts. I am using a Ranco thermostat which is rated at 1500 Watts. However, the Ranco and Johnson's that are pre-wired with a power strip can only handle 700 Watts due to the built-in protection cicuit in the power strip. I modified mine by removing the power strip and wiring in a heavy duty extension cord. So, depending on what type of thermostat you are using will determine what position you need to put the heater switch in. I set the built in heater thermostat pretty high so that it doesn't over-ride the other thermostat. As far as where to put the probe and t-stat, I did just have the probe mounted next to the tubs, but I got tired of looking at everything on the floor so, I basically mounted it all to a spare piece of melamine I had and the probe is about the same average height as my tubs. Here are some photo's:
What it did look like...
Using a spare piece of melamine from my garage, I added 2 screws and a few hooks to the front and 2 hinged brackets to the back, all from this assorted picture hanging kit I have...
Then, I just hung everything on the board and used a zip tie and the hinge brackets on the back to secure it to a desk I have in the snake room so it won't fall over...
Hope this helps...