So how should I go about figuring out whats damaged and whats working and how can I fix said damaged components, or replace themAlso the system has been in for about 9months now, I changed the grounding points 2 months ago.
Is the battery a sealed type? Most car batts are not. Have you been checking the water level in the cells regularly? The more current you pass through a wet cell battery, the faster the cells will evaporate water. If the water level is allow to drop to the point the plates are exposed, oxidization occurs and the battery is permanently damaged. If you say you have never checked the batt, I bet if you go out and look right now, you will see exposed plates in every cell.
The alt could have a diode burn out, screwing up its already measly output performance. Most local auto parts stores can bench test an alt if you bring it in (and is usually free to test).
The amplifier could also have transistors and diodes burned out. That is more difficult to verify, and many times takes an expert opening up the chassis and inspecting it.
The sub will likely show signs of a burn coil (discoloration) and as someone else said above, will diminish its lifespan considerably.
I recommend a new, higher output alt. Probably a new, high performance sealed type batt, and proper wiring throughout (I forget what you say you've done for wiring already). The stereo equipment... well, I suppose you can simply keep using it until it breaks, unless you want to tear your system out and send the items off to have them inspected and/or repaired (if necessary).
I dont mean to sound doomsday here, you may not have damaged everything Ive mentioned here. Im merely saying its certainly possible any one of those items, or possibly all of them, sustained damage. Again the main thing here is to realize the mistakes made, and not perpetuate them in the future. Good luck, and keep us posted. If you need help fixing this issue, feel free to post as many questions as necessary until you are on top of the situation.