I assume you're using a new seal?
Normally with a new seal you shouldn't really need sealer.
It wouldn't hurt to use a small amount applied where the rubber meets the bodywork though,prevention is better than cure after all....
A thin bead is all that's required and any excess(ooze) can be cleaned off with paintshop panel wipe.
In my work I use a product called Arbomast,it's a non setting,non aggressive sealer(it doesn't hurt your paint) or cause any problems should you need to do any paintwork later on.
Unlike some silicone based products.
I'm not sure if it's available in the U.S. but i'm sure you could find an equivalent.
Try asking in a local auto glass shop,they might be able to recommend something similar.
I hope this helps.
Good luck.
