Recently we recieved about three inches of rain overnight. Two poles holding up the custom cover (It fits perfectly on my Jimmy 2 by the way) were in place yet there was enough sag in the cover to let water pool and thus find its way in. Quite a bit of rain penetrated. Gallons of it.
With another storm looming I searched for a fix and flat out blundered into one. Something called a pool pillow. These things are used to "tent" tarps in swiming pools. I got a 4 X 8 foot pillow, semi inflated it, and stuffed it down the lenght of the skiff. It poofed the cover like a loaf of Wonder Bread! The storm dumped 2 3/4 inces of rain that night. In the morning I mopped out less than a cup of rain water. I took the pillow out and put the pole back in the keep things vented. When big rain hits however that pillow will be back. It might work of you.