I fought long and hard to stop my boat filling up with rain water when on its trailer, like yours the trunks are at deck level way above the lowest point.
I've now also fitted an all over cover, but before that I fitted a 3/4 inch dia drain fitting at the lowest piont in the transom, with a screw in bung.
A proper brass/Bronze one that goes all the way through.
One of these
http://www.aquafax.co.uk/html/produc...s.asp?ID=12449
It is easy to just remove the bung whilst the boat is on the trailer, don't even need to leave any pumps on or anything.
You do need to remember to put it back in though when you launch.
If not you'll end up hanging over the stern of your rib half submerged in the murky waters of the camber with Nos4r2 holding your ankles. I think you can guess how I discovered this.
Nasher