Paint vs Varnish
Paint is more durable and will protect the epoxy and timber the best.
Varnish hides a rough surface better. If you have done a rough job the timber grain will hide it. Make sure the varnish contains ultra-violet filters.
My usual plan is to varnish the inside of open boats and decide to paint or varnish the outside. Generally if you can store the boat indoors when not in use there is no reason to not leave the outside clear finished. But it is going to be left outside much of the time I would consider a painted exterior including the gunwales and remember to leave the boat upside down.
Types of Paint and Varnish
There are two basic types of paints and varnishes.
A professional finish is 90 percent dependent on getting the surface smooth between each coat - this is the BIG secret. There are no miracle methods or products.
My tendency for maximum durability and best appearance would be to use a two pot polyurethane for the outside, round to the underside of the gunwale, and a varnish on the interior. For rough use I would paint the whole thing.
Consider masking off some of the floor areas with masking tape including nice rounded corners and using a non-skid finish.
A caution with conventional Turpentine based paint over epoxy
Sometimes it is said that you don't need a primer or undercoat when painting over epoxy.
This is possibly true of two pot paints - but still it is a good idea to use a high build primer so the colour of the wood doesn't show through the paint.
But with conventional paints I've experienced a problem where the final finish paint never seems to harden if applied direct over the epoxy. It just stays wet or cheesy. The way to avoid this is to dewax the epoxy carefully (unless it is one of the newer low waxing epoxies which minimise amine bloom) then sand the finish and finally to apply the undercoat recommended by the finishing paint manufacturers.
For some reason undercoat never fails to dry properly - in my experience :-)!
New Products/Methods - Single pot polyurethane with Teflon.
I am not up to speed on it yet, but the people at Duck Flat Wooden Boats are getting excellent finishes from the new range of International brand paints that have teflon added.
They use a small (3 inch - 75mm) soft foam roller, The foam on these rollers is quite thick but the diameter is fairly small - maybe 1.5inches (37mm): in Australia they are sold under the "GEM" brand. The rollers leave a level coat and the paint levels out significantly as it dries.
One trick to to run the rollers pretty dry. If there are lots of little bubbles being left behind no matter how hard you work the surface then you are using too much paint.
The result is a little short of a good average spray standard. Gloss is excellent.
Paint and Varnish Maintenance Guidelines
Hose the boat out after use.
If leaving it outdoors for extended periods turn upside down on a couple of bricks so that air can get under it and water can run off. If the epoxy coating is damaged put three coats epoxy (wet on wet) on the exposed wood and touch up with varnish or paint.
If varnish is continually exposed to sun it will need a light sand and two or three new coats every year (more frequent in the hotter states). Two pot varnish will go for a couple of years under the same conditions.
It is important not to let the timber underneath deteriorate - the whole coating will need to be sanded or scraped off and you have to start from the beginning.
With varnish the rule is that if you are trying to decide whether it needs a new coat or not, then it needs one NOW. This attitude will save you a great deal of maintenance.
Conventional paint can be given a fresh coat when it starts looking shabby (3 years?). Two pot paints should be good for 5 years or more.
Keeping the boat out of the sun will reduce need for maintenance many fold.