I use a product called Arbomast,it's a non setting non aggressive butyl based sealant specifically intended for this,i'm in the UK but I'm pretty sure it's available over the pond too.
You can use it without removing the windshields,cut the nozzle to approx 1/4" diameter then apply it between the glass and seal and also between the seal and bodywork,don't scrimp with it,let it ooze.
Work around the seal 'massaging' it to spread the sealant under the rubber.
Clean up is fairly straight forward too,I use a thin edge plastic scraper with a mild soap/water solution to remove the excess and a final clean up with paintshop panel wipe.
