Down here tarping to protect from rain is usually not a problem. The times I have been out and we have had rainy weather (more than just a passing rain), the biggest issue was constantly dumping water from the canopy. I would anticipate that spreading large tarps over your PUP would cause the same issue unless they were set up in such a way that water was not going to pool in any particular spot; hard to do if looking at large area.
As long as bunkend canvas is in good shape, you should not have issue with water infiltration coming in the bunkends. If you need more outdoor space you might want to consider stand-alone canopies (10'x10') which would give you an added area outside.