What model skimmer do you have? CLSC, Regal, Elite?
All skimmer are able to handle having the output fully submerged, half way or completely out of the water. It is actually more important to have the skimmer in the right amount of water depth.
Without knowing what exact model you have, it is hard to tell what depth the skimmer should be but here are some of the common depths:
CLSC-200INT: 7.5"-8.5" water depth
Regal 200INT: 7.5"-8.5" water depth
Elite 200INT: 7.5-9" water depth
Prime 200INT: 7"-9" water depth
We usually recommend starting at the lower end of the range and then lowering the skimmer to higher water depth if needed.