Ball pythons don't need a separate feeding area, so no worries about that.Moving them to feed could even potentially cause issues and cause them not to eat.
The thermometer probe (not the thermostat probe) is fine just under the substrate. The thermostat probe should be UNDERNEATH the cage, between the UTH and bottom of the cage.
Ball pythons will burrow under substrate and lay against the bottom of the cage, so you should be measuring the temp there.
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