On the few kits I have built, all the control surface gaps are sealed. It certainly will not hurt and may help. I cover all my parts before final permanent assembly. Either way is OK. Plan ahead and think about it a while before you decide how to do it. You may do it one way on this plane and try it another way on the next plane. Application of trim is generally no more difficult either way. It may be easier to line up long trim runs if done after assembly. The windex method works great for me. After squeezing it out, work slowly with one of the small trim irons and you will find it easier to avoid bubbles. A very small pin will "pop" the bubble, then you can iron it down.