Put the quarter plugs in and tape the seam up. Fill the quarter up with "Chassis saver" and slop it around. Even up over the tops of the wheel house. On some cars we filled the front of the quarters and rockers with 5 gallons of "chassis paint" "Chassis saver" was to expensive.
Pull the rear quarter plug and let it drain into the container. Do the other side. Then continue to the front of the quarters and rockers one at a time. This coats everything you cannot get to. Leave the weep holes open in the rockers after you untape them. The plastic plug has it built in for the rear of the quarters for that reason. so it don't hold water. No matter what you do water will get in there. Don't dam it up. Here are pictures of some we did. As you can see they drip for a day or two after you pull the tape off.
I mostly use 3M All Around Auto Body Seam Sealer tan in color. Like it cause you can lay it in there like a nice welding bead and even smooth it out with a wet finger. Paints nice too.
A bit spendy but so are new quarter panels and the labor to put them on.