Even if the temp is lower on the bottom than the top, the tstat will still control the uth. Just instead of having to set the tstat at a higher temp to account for the upper temp you would set it lower to account for the lower bottom temp. Still works the same.
As long as the hotspot is properly checked and the temp known it will not matter if the probe is on top or bottom. I personally like to have the probe on top but sometimes the bottom just works better.
I have no clue what the OP had setup or has done with the little information we have been given and expected to help. I feel as if there is more to this story than they care to reveal.