Thank you everyone for your input. I'll be taking Jetblue to Atlanta in July. I have checked their website, and even called them and unfortunately can't get a clear answer. The following is from their website
"Ammunition for the firearm cannot be placed in the same container as the firearm, but may be in the same checked bag as long as everything is packaged properly. Ammunition must be housed in a separate container that is completely separate and distinct from the firearms locked box. The ammunition must be packaged in a fiber (such as cardboard), wood or metal box specifically designed for carrying small amounts of ammunition. Ammunition is limited to 11 pounds per customer. Ammunition will not be permitted in carry-on or checked baggage on international flights. "
I don't want to take a risk and go through unnecessary bs so I'll most likely by some ammo before the trip, and as David said... Keep an extra factory box on hand for these instances. You just never know with people knowing what is permitted, and what is not.