But back to everything I originally asked, can anyone answer this stuff or not?
1. Is there any website or link that will have a generic, or detailed, description of what I need to do in order to make this work; basically meaning how to connect the amps to the battery (I have all the wiring/fuses). Im pretty sure I know how to connect one amp up but I have no idea how to connect two.
Yes. http://www.bcae1.com. Very good and useful info. You can PM me for info about your specific car
2. Will I be able to use the tweeters and 6.5's like a component system without having to buy the crossover box? If so, how will I connect the tweeters, 6.5's and 6x9's (6 total connections, with only 4 channels being available)
A componet system typically comes with a passive crossover. I assume you are using a spacer to fit the 6x9s in the package tray as they don't fit under normal circumstances. You can hook the front two channels to the crossover, which will distribute the power to the mid and tweeter. Use the rear channels for the 6x9s. Run all new wiring.
3. Will I be able to still use the stock radio, but also use the upgraded one, possibly adding a switch or something to go back and forth between the two for car shows (though I haven't yet entered one) and whatnot, or even just being able to use them both at the same time. And if THATS possible how do I connect both units to the whatever power source is powering them.
It is possible using a switch. I would not waste my time with it. If the radio is new, it probably only carries AM stations (FM was rare option).
5. I'm planning on using the cap on the subwoofer amp only, however, is it capable of storing power for both? If so, how is this connection made?
Don't use the cap.
6. Will I need to upgrade the alternator? It is currently powering the normal, stock components of the car. I can not find the model # or any other information, besides the brand (Motorcraft), on it, its not on the casing, and I don't have the box anymore(sorry, I know this first part of the question is probably unanswerable). Also, the current one uses an alternator regulator, can I remove that, or buy a different one that is a higher rating, to compensate, instead of buying an entire new alternator? Or can I buy another battery and make a connection so that the alternator is powering both batteries?
You can buy a higher amperage alternator. I am unsure if the equipment you are running will require it. jegs/summit racing will carry one for your application.
7. Can I use the Boss head unit to power only the 6.5's and the tweeters, while the 1400w amp powers the 6x9's, and with that can I use the left over 600w's, in correspondence (possibly bridging, though I don't know how to do that) with the 1600w amp too? That would have the total wattage going to th two 12's at 1100w's each, 100w's below the 1200w peak, the 6x9's full powered at 400w's each, and the 6.5's and the tweeters powered at approximately 100w's each.
No tweeter I ever heard sounded good at 100w. See the suggestion above.