Ok, most aftermarket units have a hookup for power antennas on the wiring harness so that it's only up when the radio is on (vice cassette or cd, when it's not needed). If your unit doesn't have this, you could always run a splice from the radio power itself or anything else that's on while the car is on and it should put your antenna up when you turn the car on and off while the car's off. I'd have to look at a schematic for the antenna because it likely has a power hookup and a remote switch to tell it to go up and down. If this is the case, you'd have to run a battery hot wire to the antenna so that it put itself down after you shut the car off, plus one from the radio to tell it to go up and down.
Simply, if your aftermarket unit is designed to work with a power antenna, it should be easy. If not... I probably wouldn't bother. Well, I say that, but I'd probably get creative. If you're not electrically inclined, I would probably shy away lest you become the DPO.
Phoenix | 72 MGB