I have a Logic CP620 amp on a MTX Blue Thunder 12. I have been tweaking the settings a number of different ways because there are times when the bass really hits i hear a noise like someone is thumping the cone. i know that this is probably an over excursion of the cone. any ideas on eliminating this?

that is probably the sub bottoming out. Basicly the coil is hitting the backplate of the sub. Which is not good at all. You need to adjust your settings so that doesn't happen.

If its not that then it is likely the amp clipping, which is really bad also.

my amp has a built in crossover. i have it set at 155 hz. and my gain is at 310 watts. what do i need to change here?

do you have a link to your amp? This is the first time I have heard of gain measured in watts and not volts.

37Hz - 150Hz is the frequency response on the sub. My head unit has a front image enhancing feature on it that cuts all the lows to the rears and all the highs to the front. There are three settings for it. 100 hz, 160 hz, and 250 hz. I had it set to 160 hz plus my amp was set to 77.5 hz. So my if you do the math that was higher than the max frequency response for my sub. I put the F.I.E on 100 hz and turned the crossover down to 17.5 hz and it sounds good.