Maybe someone in the building cages/enclosures forum can help you better! Flexwatt on one side of the enclosures especially if you can do it so the flexwatt is on the floor rather than the back should provide enough belly heat. You shouldn't need a spot light on top of that for leopard geckos (assuming the temps are fine inside just from the flexwatt). I'm not sure about the thermostat control unit though if its based on total watts you should be fine since flexwatt doesn't use much.
I haven't built a cage in many years and never for leos though, so be sure to double check anything I say! Sounds like you're making a really nice set-up there. Remember to use a non-toxic sealant like liquid verathane (I think that one is safe). Again, people in the caging forum will have more info for you.
Good luck!
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Andrea A. 