I just brewed a 12-gallon extract Hefeweizen and checked the temp of the room where i am keeping the carboy, it is 59 degrees. How low is too low for problems to start in fermenting? Also is there anything i can do like put a towel over it to raise temps?
You need to be concerned with beer temp, not room temperature. That said, hef generally likes to be a bit warmer for flavor development. Fermentation will raise the temp a bit. Using a towel will help hold that heat.
Having a 59F basement sounds like a luxury, but as mentioned, its the temp of the fermenting beer that matters. For a Hefe, the best fermentation temp is about 62F for a more clove-focused expression. But you can bump that up by a degree or two if you prefer more banana expression. I find that 63F is pretty nice.