Put the glue on the side of the foam that is staying flat. Instead of in the middle of the cavity. So on a B fold, put the glue on the edge of the bottom plate foam. That way when you fold the side up it will sit flatter.
One trick you can try, if you can still get to the joint, is to apply a thick bead of hot glue along the opening of the joint to re-heat the glue inside, then using some scrap foam (cut several scraps before you start) scrape as much of the new glue out while reshaping the joint. just be careful to keep the glue out of the notches for the power pod (on the speedster you can cut the glue out before you install the turtle decks, but it's a pain to do).
Keep in mind, the top will be covered by a posterboard turtle deck, which will hide a lot of this. Looks are nice, but the big concern for flight is keeping alignment between the wing and the tail. Ugly planes still fly beautifully
Heating the joint with a hair dryer (on low heat) should soften the glue enough to allow you to flatten it out a bit. I have used a hair dryer to separate parts that were not glued straight. Be careful not to apply too much heat to the foam.
I have found an iron on low heat can soften hot glue enough to re-work a joint without melting the foam. I actually use my covering iron, but a household iron would work too. As Jaxx suggested, a hair dryer would probably work. Do not use a heat gun, it will melt the foam. Ask me how I know this.
I mentioned that I like to use a monocote iron. Even if you apply glue to the bevel cuts for ailerons, elevators and rudders and they are stiff as you applied too much glue. Open the joint and iron the hot glue. You should be able to iron the outside of the joint to soften the glue and reshape the joint. Just my 2 cents.