Hi,
No you want them all to be controlled by the thermostat to prevent overheating.
The dimmers will simply mean less power gets to the top ones when the thermostat is providing it meaning they will not get as hot.
It will take a little tweaking at first but once you work out the set point on the dimmers the whole system should regulate itself perfectly well under the control of the thermostat.
Oh and save yourself some heartache by testing the dimmer switches on a lamp first and marking the dimmer in permanent marker with which way is turning the power up and which way is down - sounds stupid but it is a real pain to try and work that out reliably on a heatmat.
If you test it on a bulb you can see instantly and you then also know the dimmer works. This can save time is you wire it into the heatmat and nothing happens as you know both components work so it must be the connection between em.
dr del