put fondant sided on two opposite sides then rool out enough fondant to lay over the top and other two sides and leave enough to tuck in over the fondant peices that you first put on. I would practice wrapping a box exactly the way you would the cake(not moving it around to cover all sides) to work out all the kinks. The hardest part is going to be rolling out the fondant big enough to cut a large rectangle the right size for your box/cake and getting it on without stretching it out.
I would just use a flat edge to indent the sides to make it look folded. If you did your fondant the right thickness, you could certainly score in this folded look and then make it deeper for the fold that was 'under'neath.
I hope this make sense.