The bubbles that form between the covering and the solid balsa surfaces when you use a heat gun should go away as the covering cools and the trapped air goes into the wood. Make sure not to get the heat gun too close to the covering and don't try to go too quickly. If the covering is on top of another layer of covering like a trim piece, use a low iron heat setting to iron out the wrinkles. You may need to use a very small needle to allow any trapped air to escape before re-ironing. Also be careful around decals, since they can melt or distort if they get too hot.

Good Luck...Len