If you park nose-down, and water runs down the rear roof and pools against the seals between the shells, the seals should not leak. But "should not" is not entirely comforting, at least to me. In your situation, I would buy an 8' foam log, either square or round cross section, maybe 6" or so in diameter. Put it on the rear roof, just behind the seal, and stretch your cloth cover over it as you cover the trailer. This will force surface water to flow back and off the sides of the trailer, rather than pooling against the joint between the front and rear shells.
The above is just a mental picture, of course. If you can't find an 8-foot log, buy two 4-foot logs. If you can't get 6 inches, then 4 inches is probably adequate, though larger is better than smaller. Buy a rigid foam, rather than soft. If you really don't like the log idea, then how about a piece of plywood 12" wide by 8-feet long, covering the seal area under the cloth cover? I don't like this idea as much as the log idea, because the sharp edges of the plywood will tend to rip and shred the cloth cover, especially if there is any wind.
But you get the idea - redirect the water away from the joint, so that it can't pool there. By the way, you can buy the logs, called "foam rollers", in a sporting goods store, but they are really expensive. Look elsewhere.
ScrubJay's caution against plastic tarps agrees with everything I've ever read. Buy something that breathes.
Bill
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