Unfortunately, if your son has been in Georgia for 6 months and he has not yet been back in North Carolina for 6 months, the father of the child can file for custody in Georgia. The rule for jurisdiction is that the child must have resided in that state for at least 6 months prior to the proceeding for that state to be considered the child's home state. It sounds like, from the facts that you have given, that the child's home state, at least for now, is Georgia. Which means the father can file for custody in Georgia and Georgia will have jurisdiction.
The laws regarding jurisdiction are a little complex. The simple answer is that the "right" court is the one in the state where the child lives at the time the case is filed or where the child has lived for the last six months. Situation like yours are a little more difficult. And there can be TWO states that are appropriate. It sounds like you were in NC before the break up. You have been separated for 3 years. You said he was with you most of the time in NC and only when to stay with his Father when you were on bed rest. That time could be argued to be a "temporary" absence and not make Georgia the place to decide custody. If the two of you are in agreement that the child live with you during the school year, and with him in the summer, then I feel NC is the best place to file the action and resolve the matter. And I think you have grounds to argue NC is the child's home state and Georgia was only a temporary absence. But if he is going to file, he may pick what is convenient to him. You should see a lawyer and consider taking the reins of this action to make sure it is in NC.