Ok my amp has two bass boost ****. One is bass boost frequency and the other is just bass boost, the bass boost frequency is 32 to 64 HZ and my box is tuned to 40 HZ does that mean that i should set it at 40?

I don't use the bass boost on my amp because it adds to the chance of the output signal clipping. But if I were to, I'd dial it a bit lower than what my box was tuned to. Try listening to a song with alot of bass and see where it seems to be lacking. In the lower note range or higher.

Well i think no matter what i do to it it will still not sound like i want it to since my electrical system isnt upgraded. No matter what when it hits heavy notes i can watch my battery gauge go down, almost into the red, which leads to distortion so the louder i turn it up the worse its gunna sound.

if you are spiking that bad, you need to fix it NOW!!! that could lead to damaging your amp and sub and battery. id buy a HO alternator asap

It only does that when im really playin it loud. Until i get my new alternator im not going to play it that loud, theres a max buttom on my cd player when i turn that on it tends to dim everything when its off it doesnt. I just cant afford a HO alt right now. I was wondering if i were to get the alternator if i could run it off the stock wiring for awhile until i can afford 0 gauge.

manufacturers recommend upgrading. You really should do at least 2 ga