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Building a Weekender.  I have predrilled and screwed in the rub rails.  Here is my question/concern.  Not sure if I need to "seal" the screws in any way to prevent water entering.  Here are some details.  My rub rails have a "channel" routered in the middle of it.  This allowed me to screw the rub rail into the boat (as opposed to screwing blindly from the boat to the rub rail).  Also, I made this channel to install rope in it for not only a salty look but also as a sacrificial rubbing surface.  The rope is nailed in with brass tacks.  Another important detail.  The backside of the rub rails are not laying against the boat hull perfectly because of imperfections (i.e. epoxy drip marks, etc.) on the backside of the rub rails.  Therefore there is a minor gap here and there between the rub rail and boat.  Last detail.  I predrilled the holes and then used #6 1 inch stainless steel screws.  Any thoughts as to IF these will leak eventually?  I thought about dipping the screws in epoxy but that is impractical....I can't work fast enough before curing and I believe most of the epoxy will be in the rub rail screw hole and never make it to the boat.  Also, I have an extra set of rubrails should I ever need them.  I'd rather unscrew and replace then chisel.  Any thoughts?  Anyone have leakage with just screwing into the hull?  Is there a difference of what direction the screw was screwed in? 
Slight revision.  Upon further reflection....I think it is a stronger bond if I screw from the inside into the rub rail (going from thin to thick instead of the other way around) AND I just realized I have sharp screw heads inside the boat.  So...I am going to back out the screws and screw them in from inside the boat into the rub rail (at least I'm not screwing them in blind now).  So.... thoughts on just dipping screws into silicone to help prevent water coming in?
I usually have an "inwale" backing up the rub rail on my builds, to prevent having a too thin a material, supporting the rubs. In your case, fastening from the inside will be the strongest. Also consider using panhead screws, with bigass washers under them.

Start out by figuring out where they'll go and pre drilling the hull and rubs with pilot holes.  Slightly countersink the holes on the outside of the planking and the inside face of the rub rail. This is an old boatbuilder's trick. You see, rub rails are bedded, typically in polyurethane or polysulfide (prefered on wood) sealant (caulk). This bedding goo will fill up the countersunk areas at the interface of each fastener, where they enter the hull planking, forming a gasket/"O" ring sort of deal. Use too much bedding goo, you can always wipe off excess.

On thin planking I often use machine screws (mini bolts) instead of screws, again with a big washer. In some places, fastening from the inside can prove tough to get a good angle for the drill and driver. Fastening from the outside can solve this, but you have to bung or otherwise hide the fastener heads (if desired). You groove idea will work well and it's how the manufactures hide their rail fasteners too.

I usually don't use rope, because it just doesn't stay put unless glued and fastened, but it is cheap. I like to use plastic or rubber hose in the groove instead. The fasteners are insert through a tiny slit (exacto knife) at each location. Once the fastener goes through the outside hose wall, the slit closes up and disappears. In most cases, I just use metal strips (half oval, aluminum bar stock, etc.) to serve as the actual abrasion piece. These too are bedded in goo and lightly fastened, so the fasteners fail, before major damage is done to the wooden rail below. It's easier and cheaper to replace the sacrificial rope, hose or metal strips than the whole rail assembly, so use short and little (#6) fasteners.
Thank you for the insightful reply.  I will follow your recommendations.  One question....I was going to use 5200 or 5300 between the boat and rubrail instead of bedding (in addition to screwing it on of coarse).  The Weekender is fiberglassed and painted.  Thoughts?
3M-5200 is an aggressive adhesive/sealant. I works good, but it's also so tenacious as an adhesive, it'll rip up sections of boat if you ever have to remove it (you will). I dislike 3M-5200 for this reason. 3M-4000 is a little better, but not much. 3M-101 (polysulfide) is much better. BoatLife caulk works very well as does DAP Dynaflex 230, which is available at the big box stores and is nearly as good as the special marine caulks, but much cheaper. When looking for these types of sealants, read the label and look for the terms "waterproof" (not water resistant), "mold/mildew resistant" and of course rated for "exterior" uses. These will perform well in above water applications, usually a lot cheaper than the marine rated stuff.  If you need an underwater product, use 3M-101. Lastly, I'm sure it's a typo, but 3M-5300 is a blue scrubbing pad, not an sealant. There's also another 5300 3M product, but it's a high voltage wire splicing kit.
I had the same concern with it being too adhesive like.  I will go with the 3m-101.  Thank you for the help.