We're new to the hobby and experienced a similar problem when we first set up our habitat. First we were told that we should be safe using a 6x23 Ultratherm UTH without a thermostat 'because of it's low wattage". When we couldn't get the belly heat in our hot hide to the proper temp we were told that we probably should reduce the depth of our substrate.
It was then it occurred to us that regulating belly heat by adding or removing substrate made no sense. When we actually measured the heat generated by our UTH directly on the bottom of the habitat (110 degrees!), we realized that it not only didn't make sense, it was dangerous.
So... we added a Herpstat, set it to 92 degrees, and lowered the substrate around the hot hide to about 1/2" (our boi usually pushes it out of the way). The rest of the habitat has 1" or more of substrate, which does help with the temperature gradiant. A 40w CHE manages the ambient temp.
Basically, our first lesson was that substrate looks pretty, is useful for managing humidity, but it should never be used to regulate temperature.
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