cut a oval where the stacks will go through and then weld a piece of flat metal ( diamond plate looks great) onto the stacks where the hole is cut and put some GOOD sealer of some sort a good rubber strip will work if its a little ways away from the stack.. make it so that when you close it the rubber piece places up under your bed cover and seals it from the rain ive done this on a tool box never on a bed cap but its the same principal i would post pics but the truck i did it to was wrecked about three months ago and long gone