Q: Are you not supposed to exercise sore muscles at all or just not within the 48 hour recovery period?

A: Don't exercise sore muscles at all. In most cases you'll be ready to go again after 48 hours, but sometimes (when beginning a new program or exercise, especially) the soreness will stay around longer. Wait till it's completely gone to exercise that muscle again. In the meanwhile, you can exercise your other muscle groups that are not sore.