No need to run the battery down before charging as long as you are charging at 0.1C (the typical wall wart charger that came with your system). They will not harm your battery even if you leave it on for several hours more than the recommended 12 to 15 hours. This is assuming you are using NiCad batteries. See Red's site
www.rcbatteryclinic.com for some good honest and common sense info on batteries. More planes are wrecked by undercharged batteries than over charged ones.