There are several possiblities:
1.) The alternators with more than stock output need a 4 gauge wire & 125-135 amp fuse from the alternator to the battery post of the starter solenoid. You can get the fuse & wire at the local auto stereo shop or try
www.partsexpess.com. You will need to assemble the wire & fuseholder on your own. However, there is kit from PA Performance if you want to spend the $$$. Or you can use the battery cables with the lugs crimped on the end if you get the wiring from the auto parts store.
2.) Do you have underdrive pulleys? If so, get a smaller pulley for the alternator.
3.) High output alternators need a separate 4 gauge ground run from the engine block to the chassis ground where all the other ground wires for the battery connect. The best place on the engine block is the ground by the oil filter.
4.) You have some device that is drawing power when the engine isn't running. This could be a badly wired alarm system, stereo, or a courtsey light that stays on all the time.
The ideal method is to disconnect the positive terminal, and connect a Digital Multimeter (DVM) between the positive terminal on the battery and the positive cable. Set the DVM on a low current scale of 2-5 amps if it doesn't auto range. Watch the current draw, and then start pulling out fuses. When you see a sudden drop in the current, that circuit is the likely culprit. Note that the computer, radio & clock will draw less than 1/10 amp to keep the settings alive.
If you don't have a DVM, a test lamp can do the same job. Just connect like I said to do with the DVM. When you pull the offending fuse, the light will dim or go out.