I would use a PU based seam sealer applied directly to the body, via a caulking gun. then using a cheap 2 inch paintbrush to bush it in. If you look under your car, you'll see areas that have been done in this way from the factory, the secret to make it look like OE, is to not stipple the sealer, but brush it with one stroke... leave it to dry for half a day, then give it a light coat of primer, followed by a light coat of body colour, blending it in to match the original, if thats the look that your after that is?
Finish the underneath with a clear based Waxoyl, VWs own product is very good, and can be bought from the dealer for about £12 per ltr, and gives a great OE look...
Thom