The main difference between a regular bunk and a twin over futon bunk bed is the mattresses. Regular mattresses have an internal frame, which means they do not curl. Without that internal frame, a futon mattress sinks through the rails, and must be supported by a grid or a set of bars. Although different brands and models of futon bunk beds have different mounting details, most follow the same general plan. The construction will be much easier if you have a partner to sustain the constant frame as you work.
Set the pieces for your futon bunk in your work area. Place all the nuts and bolts that come with the bed in a plastic container. Adjust the end pieces of the bunk bed frame in place, approximately where they will go to bed when it is complete. Leave at least 12 inches between any of the edges of the frame and the walls, so you can move while you work. Install the lower mattress frame. Set it in place and fix it with four or eight screws, depending on the model. Slide the bolts with the heads pointing outwards.
Tighten all the nuts on both frames by hand until you can no longer move the nuts. Tighten the nuts further by holding the nut in place with the key or locking pliers, then screw the nut into place with a screwdriver or a hexagonal wrench. Attach any railings that accompany the futon bunk bed.