Thru bolts only, lag bolts will fail before long. Covering on all sides will speed up the rot process. I only wrap the top and half the side when I use carpet it allows the wood to dry faster. If you used the UHMW strips of plastic, you would bolt thru the bunk then screw down a strip of plastic on the top of your bunk, three sides would allowvthe bunk to dry out, they would last for many years !!