depends on what kinda battery you have if u need to replace it. sure, its bad to deep cycle a battery repeatedly, but it depends on the make. i have an autozone battery and i accidentally drain that sucker at least once a week and i have no problems with it. MO_GUY is right, if you have a system and repeatedly work on it with the engine off, you should probably get a yellow top(im just too lazy/poor to go out and get one)
also, its good practice to start the car ever hour or so and let it run for a couple of mins to recharge.(just make sure you have enough ventilation!)