How do I align my front brake disk with the caliper? I have manual Avid disc brakes.

I took my front wheel off like I've done hundreds of times. When I put it back on the wheel is aligned properly with my fork, but the disc presses against one of the brake pads. This causes a lot of squeaking when I simply roll the bike and a ton of friction that will eventually destroy the brake altogether. This really isn't making sense to me other than the possibility that the caliper just isn't aligned properly, which seems practically impossible because all you do is screw it in. 

I have tried adjusting the sensitivity of the brakes to the point where the problem pad is off of the disc. Then the other pad is so far out that I have 0 braking power when I try to apply it (other than a little friction from the problem pad). Can anyone please help me?
It's not that unusual for a front brake to move a bit when taking it off and reattaching it. This is due to the small amount of space between the fork ends, axle, and QR bolts. The fork flexes a bit when you put the wheel back on. That small space that it moves is a lot relative to the clearance that disc brake pads have. That's likely why your brake pads aren't lining up again. 

Now, the fix (NB: the following assumes that by "manual Avid disc brakes," what you mean is "mechanical disc brakes."):

It sounds like you're overlooking a couple of points of adjustment. There is a red knob/wheel that adjusts either side of most Avid mechanical disc brakes, one on the inside and one on the outside. There are also caliper positioning bolts (CPS, the "S" is for system) that move the entire caliper perpendicular to and directly above, the bolts that attach the caliper to the frame.

The basic procedure to properly align your brakes is to:


Loosen the bolts perpendicular to the mounting point so that the whole caliper moves easily.
Completely loosen both of the red pad adjustment discs.
Tighten the inboard pad adjustment knob until the rotor is centered in the caliper.
Tighten the outboard pad adjustment knob until the brake is clamped onto the rotor. This ensures that the caliper is centered on the rotor.
Tighten the CPS bolts.
Loosen the pad adjustment discs evenly, one click on one pad, one click on the other until they no longer rub. It may not be perfectly even, one pad may require a bit more loosening than the other. Don't worry about that as long as they don't rub. 


Here are the actual owner's manuals for your reference: Avid BB5 and Avid BB7.