Nah, I poke it under the leg or sometimes over the top. Plus the fly on boxers is often a nuisance, your dick pops out under your pants and you have to awkwardly fix it. I now get boxers which have the little button on the fly to stop this.
An unfortunate concession to sagger fashion with boxers is the material is often not stretchy, more like sheeting so you are forced to use the fly - assuming it has one. You can't easily 'go under' or 'go over' with this material, but I suppose they look good when sagging.