Good morning Mindi,
Yes, the gain settings for high and low frequency are going to be different. The LF side is subject to more interference from turbulence and other disturbances found in the water column. Typically I like to see more stuff on the screen than a completely clear picture. But everyone has their own preference. You could try to turn both the LF Gain settings and HF Gain settings to a point where you are starting to see come clutter, then you can use the Clutter control feature to suppress some of the weaker clutter returns and not sacrifice the front panel gain.
It would be good if you followed up with some before and after screen shots, also what sounder you are using and have you adjusted any other filters or features.
C-Bass