Best way? Well, while you could just re-goop and re-seal with goop that's compatible with the deck plate, I would urge you to protect the wood core at all costs with epoxy and then fill in the hole.
CBigma has informed me that the T-H Marine plates I used and recommended specifically caution against the use of polysulfide sealants, as it dissolves some plastics. So good ol' GE silicone is called for. Not sure of the precautions with 3M 4200 and plastics and not sure what Tempress advises to use, but you could check @ www.tempressproducts.com
Me? I would drip the holes full of West Marine's 2-part penetrating epoxy first. While I HATE their prices, this is a good buy, as a lifetime suplly will cost you $21 or so. You get 10 ounces of part A and 5 ounces of part B. I mix it up just a little at a time (1/2 ounce), saving small cat food tins or those little plastic cups that 2-quart powdered lemonade mixes come in. You only need a little!
I'd tape off the bottom of the holes (in case they went through) and drip in as much epoxy into each hole as they'll take using a small syringe (I get mine from my vet for free, no needles of course
). Let it set and then bed with goop of choice. You can clean out the syringe with acetone and use it again and again.
FWIW since I've discovered epoxies ... I don't use Marine-tex anymore. I HATE their mix instructions too! I now only use that thin WM stuff mentioned above or thicker 2-part epoxy from Larry @ Raka Systems, see www.raka.com
. It's 1/2 the price of West Systems and is just as good. Lary sells an epoxy starter kit for < $20. I'm loaded with the epoxy, slow & fast hardender, plus fillers and thickeners like cabosil, kitty hair, and micro-balloons, as they each have a particular specialty.
If you need it Brad, I can send you the epoxy wetting kit