Waterproofing (or damn near) the Bed with a Cover

I just put on a trifold soft tonneau cover the other day and drove in the rain and the inside had all kinds of water running down the inside. But it looked like it was mostly coming from under the bed rail covers and such, and not from where the tonneau cover lays on top of the bed rail covers. I installed the foam pads between the bed front rail and two front corners. I see some gaps in the bed corners and wide open seams back at the tailgate. Does a man need to apply some type of sealant to block most of the water? If so, where? And what's a good brand thats black in color? Thanks.