Only time I ever use the fly is with boxer shorts. The fly on briefs, boxer briefs, and such is generally too complicated. I don't want to stand there for 20 seconds threading my penis through a complicated fly. I've tried leaving my penis tucked inside a Y front fly, but I found that extremely uncomfortable.
So, boxers, I use the fly, boxer briefs is over the top, jocks I usually pull the pouch to the side.