The main purpose of varnish on your wood boat is to protect the epoxy from ultraviolet damage while you are out in the sun. Check to make sure the varnish you choose has UV protection.
There are several techniques for applying varnish to your boat. Most people use the foam [[paint brush]es available at most hardware stores, some use a clean rag, some spray it on with high tech very expensive equipment.
Creating a [dust free environment]? to varnish in will help you acheive that [mirror finish]? you want for your wooden beauty. Sweep and clean the day before you varnish then wet the floor down to help keep dust from being kicked back up into the air. Apply the first coat and let it dry 24 hrs, flip the boat over and do the other side, let dry another 24 hrs. Lightly sand the entire boat with 220 grit or finer sandpaper, clean the boat off with water and a clean cloth, let it dry thoroughly and do another coat.
Quit varnishing after 3 or 4 coats and go PADDLE!!! after all, you built it to paddle, not to look at!
Others have found the polyurethane? spar "varnish like" products have worked well. Helmsman by Minwax has been used by a number of builders with good success.
Technique for using a clean rag to varnish a kayak:
Rob Macks has described success with varnishing outdoors in keeping dust off the varnished surface.
For Skin on Frame (SOF) kayaks:
Polyurethane varnishes rule the roost. Saturating cloth with a first coat takes the most varnish. Follow on coats take a little less. Many builders use between 8-14 coats of varnish.
Polyurethane varnish comes in a solvent based version and a water borne version. Either works for SOF boats. Some of the solvent based varnishes have UV protection. However, some users have noted that the solvent based urethane can be brittle and poking the fabric may lead to concentric cracks - a [bull's eye]?. [Waterborne polyurethane]? also works well for many builders, though the packaging of these products almost invariably state it is not intended for use outdoors. Waterborne poly is much clearer than the yellow tinted oil based poly products.
For all polyurethane based varnishes it is very important to follow the directions for minimum and maximum times between coats, and for the curing time necessary after the last coat. Typical times for water borne varnish are timing of the coats between 2-6 hours apart, and a final cure time of 3 days. Occasional posters have noted that especially waterborne polyurethane which is not allowed to cure may peel off after use.
Discuss varnish and varnishing techniques: /talk