Should I fill up a double boiler or leave an air gap?
What you do depends on what you are doing.

There are sauces where the directions specifically call for "over boiling water" (as opposed to "in boiling water") which imply a gap. Heating soup is probably somewhat less demanding in requiring gentle heating, though a ceramic inner pot will slow that down anyway.

However, the first thing to try would be just to turn up the heat a bit - steam is a very effective heat transfer mechanism, so if you have a good boil in the lower pot you should get effective heating of the upper one, even with a gap. If the lower pot is only simmering you will get poor/slow heating of the upper one.

If the lower pot is too full you may get boiling water spurting out between the pots, which might be hazardous.