I made a KTBH with the entrance on the end originally. It worked okay, although bees don’t seem to build perpendicular to their entrance when left to their own devices, so I moved it to one end along the side. That was because the bees will keep their brood near the entrance and their stores away from the entrance. That worked very well until the bees decided to abscond.
When you say you are going to add a screened section, I presume you mean #8 or 8 squares per inch hardware cloth and not window screen. If you do that, the bees can clean out that way. Bees that die in the hive are typically carried out and flown away by the bees.