I prefer to assemble first and then cover.
It makes covering a little more difficult, but the end results look so much better.
I can remember when ARFs first hit the scene. Two of the things that just bugged the hell out of me (aside from the poor quality of early ARFs) were the plastic parts (like wing tips, stab tips and a fin tip) that were just glued on after covering, and the big open seam where the stab and fin met the fuse (Due to being covered first and then assembled)
Besides, with MOST kits, assembly is done long before covering, so to cover first would require some re-engineering on the part of the builder.
The trick to covering a plane with installed tail surfaces is to iron a thin strip (About 3/8" ) to the corner first.
Below is a pic of how it's done and a pic of my current covering project with the corners covered
It is also demonstrated in the first video in this article:
http://www.rcuniverse.com/magazine/a...article_id=726
Edit: PS, Although ARFs have come a LONG way in quality, they still have those big ugly seams where the stab and/or fin meets the fuse. To me, covering after assembly is a "Badge of Honor" so to speak, that shows it was BUILT and not just ASSEMBLED