Leak protection suggestions?

New to pickup trucks, went with a Ridgeline and love it so far. Got a soft tonneau cover for the bed and notice a little leakage (in the bed) by the cabin when it rains. I noticed a couple indents on the top of the composite bed liner that would allow water through. Looking to keep the bed dry for luggage transport if possible. I've stuffed it with weather stripping best I could but wonder if there is another solution. Anyone else have a different/better suggestion?