2007 Cobalt won't start?

I recently got a flat, got it repaired and changed it all out. When I was putting the spare tire back in the trunk, however, I hit a cord that went to the battery which is in the trunk of the car(interesting design). Anyhow, I didn't think much of it and went back, closed my sunroof and noted the very strained sound it made. I then started the car because I was afraid it might be getting low on battery since I'd had it on but not started the entire time I was changing the tire. It started after a little struggling and I was all happy. A few minutes later when I tried to start it again, however, it displayed the check engine light and the theft deterrent light, the latter of which is supposed tobe disarmed by starting the car. Not only that but the check system charge light is also displayed, it's possible my car may only need a jump but seeing as all things electrical are still working in fine condition, I'm wondering if anyone's had a similar experience or knows what to do?