Heres my trick..
Map out the area you want to cover and poke tiny pinholes in the covering about every 1/4" on the layer you are covering over. The new monokote sticks right over it and the air escapes out through the pinholes. Works great for me, I just try to make the pinholes as tiny as possible pushing only the tip end of the pin through. Also, if you get 1 bubble you can pretty easily poke a hole through the outer layer without going through both and then just iron the bubble out. If you do accidentally go through it wont hurt. As long as its only a pinhole and you dont overheat the monokote any more than it takes to pul out the wrinkles.