From what I read in the manual they need to be on top of the varnish, it didn't mention any special prep. I plan to do the same thing, please let me know how it works out.

  I put my automotive pinstriping on top of the varnish. It sticks really well and when it does get dinged up it is easy to replace.

   Would under the epoxy work?

I would not put automotive pin stripping under epoxy because the epoxy does not stick well to vinyle and plastics so you risk delaminations. If you wanted to go with that route you could use posca pens for pin stripping and epoxy over or you can use colored epoxy for pin stripes and then it wouldnt mater if the stripping is done under or on top of epoxy. But you would need to learn how to tape for pin line and when to pull your tape. I used to pin line surfboards and believe me it's a heck of a lot easier to just use the automotive pin line tape. Remember epoxy does not stick to vinyl but the vinyl tape sticks very well to epoxy.  

Agree with Wood Ogre.  Automotive strips are very easy to apply after paint/varnish.