adjusting subs/HU or amp

does it make much of a difference whether i turn the gains on the amp up and the leave the HU at 0, or keep the gains lower but then adjust bass up or down with the HU controls?

Here's a tweaking process for getting the most out of your sub(s) and amp(s) in which the most clear bass possible is out main goal.
Pick out one of your favorite CDs that has a good mix with some low bass.
1. Set the bass settings on your headunit to "0" and make sure the bass boost is off.
2. Turn the gain all the way down on your amp, and turn off any bass boosts.
3. Put in your CD/Tape/MD/MP3 and choose your favorite song and put it on repeat.
4. Turn up your headunit (HU) volume until you start hearing some distortion from your speakers.
5. Once you hear the distortion, turn it down a little bit, just enough so that the distortion is gone. Here you should have the most volume without disortion.
6. Now time to get the bass going. If the amp has a low pass filter, set it somewhere between the range of 70-120 Hz. Still no bass boost yet.
7. Turn up the gain control until you start hearing very little distortion from your sub(s).
8. Back off on the gain control just a tad bit, until you hear clean, deap bass with no distortion.
9. Now you may use the bass contol on the HU to adjust the bass from the driver's seat.
Now you should have the most bass, mids, and highs all at the same time without distortion.