Julie,
I replaced my rub rail this spring so I can tell you what needs to be done. 
Where the two hull sections meet, is covered up with the rub rail. The pieces 
overlap and are level at the bottom. The factory uses a sealant at the bottom 
to seal the joint as opposed to using something in-between the pieces. The part 
of the rub rail that the rubber piece slides into covers this lip and also 
the caulking. To properly reseal this seam, you would have to remove the rub 
rail and recaulk. The simple solution is to simply caulk in the areas that are 
currently leaking, applying a bead to the hull and rub rail and then smoothing 
with your finger to push as much into any voids as possible. I would not use a 
silicone sealant as it will only adhere for a short period of time. Silicone 
is better for compression joints.
Hope this helps.

Rummy