I never tow with the cover on. The cover is like a sail and creates drag - that drag also causes the cover to beat around, put pressure on the seams, and wears it out prematurely. Plus a cover rubbing on the gel coat isn't quite a good thing either - causes scratches if it isn't 100% clean and waxed.

As for dirt and such in the boat, it's made to be outside...that's why it has outdoor carpet. If it gets wet, so what. That's what it was made to do. I really haven't ever had any road grime or rock chips to speak of either; the truck does all the blocking of that stuff.