If you are covering a flat surface, I recommend pulling the covering as tight as possible and only adhering the covering around the perimeter with the iron. Once you have the perimeter attached securely, stop using the iron. Next get the heat gun and tighten up the interior of the covering. If you use the iron to go over the entire surface, then any imperfections will be brought to the surface and you will also run into the potential issue of bubbles that you are experiencing.
The image below is an example using this technique with Monokote. I was rewarded with 17 appearance points at the 2014 Nats using this method.
Congratulations! That beats my (and maybe Allen Brickhaus') record of 15. Or at least we thought it was a record.
Everybody else - listen to Jason. You cannot use the iron in the middle of the surface or you will get some spot stuck hard and others not, and it will look awful, almost no matter how careful you are. Even if you use a "sock" over it.
The late Bill Fitzgerald (David's dad and Ted's long-time coach) was a master, and both he and I would adhere the monokote in the middle of the surface using a heat gun and a very soft cloth, leaving plenty of gap at the tips for the air to escape, and work from the root to the tip - all AFTER it was stuck everywhere else around the perimeter, shrunk without touching it, and otherwise perfect. If you don't do that, it tends to look really great at first but will occasionally wrinkle up afterwards.
And ultimately, sun exposure will cause it to become extremely brittle or even chalky, like loosely compacted powder that will pull up at the slightest touch. I took my backup airplane to the 2006 NATs and held the elevator in place with a strip of very-low-tack masking tape. Went to pull it off, and all the monokote underneath just pulled up with it like it was made of talcum powder. Later still, I was just wiping it with a rag, and it pulled a slight wrinkle from the friction, and it cracked.
Brett