I fully dischaged the battery, not knowing that was a problem, and left it for about 2 weeks. I also left the charger on for that time period, the charging status light always blinks green even when I charge the battery. Yesterday I hooked up the battery(correctly) to the charger and left it over night, on 3a, with the light blinking green, this morning I took it off and plugged it up to the phatom, and nothing. I looked up that fully discharging the battery is not good, but it seems as though the charger is what's not wrking, how can I get it working again??

well, try hooking up another battery to the charger and see if it can be charged, or try charging the battery with another charger.
PS:  You're strongly not recommended to fully discharge the battery and leave it for 15 days. Meanwhile, DO NOT leave the charger on for that long time.