1994 Honda Civic Alternator

Maybe I did not make myself clear the car will crank and run with the alternator hooked up it just runs bad the idle is bad it will not rev up it sounds like it is not getting any gas it does not go dead it runs bad but as soon as you unhook the alternator it runs great untill the battery runs down but it runs it revs up like it supose to idles good it gets gas when you accelerate the trottle, but if ya hook the cable on the alternator that runs to the battery not the four wire prong at the alternator but the single cable it drains power from the motor the old alternator was doing this allso that is why I replaced it with a new alternator. I am just wondering what is shorting out too pull power while alternator is hooked up, I know that the car can not run long with out the alternator but while the battery has a charge it runs great till ya hook back up the alternator does this make any better sense