2-channel amp question

you need to take into consideration what the rms of your sub is  and the size of your amp! too little power is sometimes as bad as too much! are you underpowering your sub or overpowering it?turning both gains down is the best scenario if you are overpowering it!

What kind of amp is it?  Is it a gain control (ie: output level) or is it the input sensitivity control?

You are probably hearing distortion from driving the amp into clipping: gain is too hign, ir input sensitivity is too high.  Turn them down.  Set them equally.

"Undrpowering" will not damage a subwoofer.  This is a myth.  The problem with underpower is the tendency to turn the gains up too high and damage either the amp or the woofer from the clipping and distortion that results: exactly like you have apparently done.

Set the inputs and the gains properly and the system will work fine.  If you want to go louder, you'll need a larger amp.

turn the gain(s) to the lowest

then turn the music up, then play with it...make it sound good to you.