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I must admit, i am not a body guy... but if you know that water is getting into teh rocker panels, then i would take a look at the bottom of teh rockers, there should be some sort of drain there. If you don't see any, perhaps drilling a few along teh length where they are not visible with a 1.8 inch drill bit might help tresolve the issue. If you do, I would recommend using a tube or touch up paint (about $5 from the dodge dealer, and it will match perfectly) to paint the edges of the holes. this cant be any more detrimental to the vehicle than alowing water to lay inside the panels and rust them from the inside out... There are also usually similiar drain holes in the bottoms of the doors.
Perhaps taking the car to a local body/ collision shop for an opinion may be insightful... often tehre are TSB's out for various leaks such as yours that we general techs dont see. If it is a common problem, they may have a quick fix for it.
I hope this is helpful; if so, clicking my accept button would be most appreciated.... thanks!