I had to remove mine when I installed my Mad Frog Gear Sideboards. They are pretty simple to remove, 4 bolts and you may have to take off your side boards to get them all the way out.
As for what to seal them with, I would get some black starboard material and some foam gasket material to do the job. If you can't find starboard you can buy black kitchen cutting board from Walmart or Target that will work just fine. Use the existing back plate that is on the holders as your template. Put foam pad between both for a water tight seal. I found the foam material in the hobby section of Walmart that was the perfect size. Its about 1/8" thick and black. Use 3m spray adhesive to stick the foam to your custom plate and to the back plate.
That should do the trick!
2011 Hobie Pro Angler
Rigged for War!