I believe that they are more efficient in a trickle but will still get the job done submerged. I have bio balls on trickle and then scrubbers in the bottom of the sump. I hope this helps. I have read that there are 2 different types of bacteria and the type that grows in an oxygenated environment removes more ammonia and nitrites. Don't quote me on this I'm not a scientist.
The conventional wisdom is that scrubbies are best not submerged. If you want to submerge your bio media, there's other media (like seachem matrix) which will be better.