What should I use to re-apply the trunk seal on my beater Neon, there's water in the trunk. Do I apply it to the seal or the edge of the trunk? Thanks in advance.

I use 3M weatherstrip adhesive, comes in Black or Yellow. Stuff sticks to just about anything. I apply it to the panel and then set the seal onto it. Press and hold for a few seconds. I usually leave the trunk open for a while to allow the glue to set. You can buy it at most parts stores.

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I haven't looked at a Neon trunk in years, but if there's a flat flange that the seal attaches to, make sure it's not bent down or away from providing a nice seal.
I do recall seeing some of them with water leaks into the trunk; sometimes back glass, or tail lamps, or hit in the rear.

Don’t do it. Those seals grip to the edge and require no sealer. Sealer is for seals that rest on the surface. A fresh factory seal will do the trick, but I doubt that’s where the water is getting in. Depending on the year, neons are known for leaking around the taillights and through cracks in the body seams. Pull the carpet, drop the back seat, lay in there with a flashlight, close the lid and have a friend hit the car with a water hose. Shoot the taillights and around the undersides and wheel wells where the seams meet. I bet you’ll find a leak.