Banjeezie,
I know we will all gladly help you as much as we can on the forum, but I would suggest that you find a local beekeeper who can take a look at your hive with you. I know that this could cause a hot debate but you have made it harder on yourself by starting with foundation-less frames. If you don't keep a close eye on your bees and inspect often, they can make a real mess in the hive just like what you described. You will have to remove that bad comb and replace with new frames. You should also make sure you keep your frames perpendicular to the ground when you handle them so the comb doesn't dislodge itself. If you have some good drawn out frames that are nice and straight, place the new empty frames between them and this will help the bees to draw the new frames out straight. Don't worry about harvesting honey. Right now you need to get your hive nice and strong. Once they get those three mediums filled out you can think about harvesting that fourth box. They will likely need three mediums for brood and stores to make it through the winter in MS without help. You should be in a good honey flow of Chinese tallow right now so if you get things straight you might have that fourth super before you know it!
As for ants, I have used Amdro bait granules in a container with holes the bees can't get through placed underneath or near the rear of the hive.