What kind of glue do you use? There are a couple of ways to get away with it without fogging them up. For myself, I use this glue I found at hobby lobby called "Extreme Power", pretty much super glue for model kits. It doesn't smell as strong, it holds good, and doesn't take hours on hours to dry. If you keep the tip of it cleaned out you can draw a small enough line that you'd be able to put those headlight covers on without them fogging.
I've also heard if you use the "model cement" type (blue tube from testors) you can use a toothpick to apply bits small enough that it wouldn't fog up the headlights.
I know your pain though. I've messed up kits before by having the lights or even worse, the windshield get fog on it
I'm sure someone better at this than me can help better though but that's just my 2 cents.