You only need to do one of the 3 below.. and then those with a little difference. I'm going to number them just like you did - but pick only 1.
1. Use only 1 coat of Thompsons. A little water is still going to seep in, and multiple coats will not allow it to dry out
2. Poly.. not much experience with this for boating, but I personally wouldn't use it
3. Deck Paint.. ok so I'm partial to this one because it's working for me. This is an exterior paint/stain that seeps into the wood and seals, repels.. You can get by with multiple coats of this because since it does seep into the wood, the water really can't penetrate it. I painted my deck with this stuff, and used what I had left over. I saw how bad of shape my deck was in (never stained, water sealed or anything). I pressure washed it, let it dry out, then put 2 coats on (lots of fun in 100* weather in the GA sun). Anyways, that was over a year ago and it's still looking like it did the day I painted it. That's been about 40" of rain, a snow storm, hail, and an ice storm. So with that being said - I'm Russ Edwards and I approve deck stain.
Either way you go, you don't need to sand in between coats. Sanding between coats of paint is for exterior shine on your boat and taking away runs and blemishes.
