Caulk!
Hey Sailoff, as everybody has stated you really have to caulk to get your handrails to seat properly so you don't get water in the cabin. The question is what type of caulk should you use? There are many caulks out on the market that would help seal out the water, but as with any product you get what you pay for. What may work today could possibly fail tommorow. In other words you've spent a fair amount of time finishing your rails (I know because I just did ours), but re-installing them is the most important part of your project and if you choose the wrong type of sealent/caulk you my find youself dissapointed because of a leak that showed up maybe not this season but next... I chose to use 3M 5200 becuase it's a sealent and adhesive and it's also very marien friendly. The problem is that since the 5200 is an adhesive, and it does it's job well, once I set the rails they will be very difficult if not impossible to get back off. Needless to say I set the rails with the expectation that they will not come off as long as we own the boat.If you feel you need to have the option to take the rails back off I'd suggest a sealent/caulk that isn't an adhesive but is meant for marien applications. Something like a high quality silicone marien sealent or maybe 3M 101 which is meant mostly for window appplications because it doesn't cure like an adhesive and will allow you to seperate whatever has been attached to the cabin with some good elbow grease. The other thing I'd suggest, to make clean up easier, is to tape off not only the areas around where the rails attach to the cabin but also around the rail itself(use a good quality masking tape). Leave about an eighth of an inch gap between where the rail will set and the masking tape, allowing for caulk to ooze out when you do you initial tightening of your bolts. As Mike mentioned, don't tighten everything down totally, just enough to get things in place where the caulk/sealent is oozzing out and the rail seems to be just about set but could use a few more turns of the wrench. When you see that the caulk has oozzed out, you can take an eighth inch dowel or a popcicle stick and/or your finger and run it around where the caulk has oozzed out. This forms a bead between the boat surface and the rail. Then I'd take the tape off very carefully and let the caulk set up for 24 hours. Getting back to Mikes point, which is a very good point because if you tighten your rails down all the way before the caulk/sealent has cured, you could squeeze all the caulk out of place or create voids where water could penetrate. So holding off on fully tightening whatever is being attached to the boat for 24 hrs. essentially allows a gasket to be formed so that when in 24 hours you come back to tighten the rails, or whatever it may be, they have something to help form a barrier (gasket) against incoming water. Good luck on your project.