Well, since I've had a couple of people message me about how to do this, I'm going to post up what I hope are clearer instructions on how to do this swap. It's really just a summation of what everybody told me to do here, so credit goes to all of you guys that helped out:
Although it seems like most aftermarket tails have just two wires, one black, one red...I believe every bike will have different colours for their wiring that you have to connect to. But basically what you should end up with from the BIKE are: 1 wire from the headlight (which will go to the "running light" or the dimmer of the two lights in your tail light), 1 wire from the brake light (which will go to the...yes, brake light or the brighter of the two lights in the tail light), and the ground wire. Since you'll be one wire short (no pun intended) from your tail light, attach a piece of insulated wire to something metal on your tail light where ever you can make a good, solid connection (you might have to drill a small hole in the base, then screw the wire to it, something like that - just remember that you have to leave yourself a way to run that new wire from the tail light through your seat cowl to the bike's wiring), then attach that to the ground wire from the bike, and you're in business.
If you need to figure out which wire is which, or check to see if everything is working the way it's supposed to, just touch your new ground wire to the negative post on the battery, and the red wire first to the positive post. If it lights up, then touch the black wire to the positive post. One should be brighter than the other; that's the brake light. If the red wire doesn't make it light up, then put the black wire to the negative post, and the red to positive. That should hopefully tell you what you need to know about how it needs to be hooked up. Since it's only 12V, you don't have to worry about getting shocked; you can just use your hands to touch the wires to the posts.
Ta-da! Good luck!