Mark, Leave it on. Mask, do all your painting, let the paint dry really well and remove tape. Then tape for the varnishing, etc

Thanks!  That is what I had hoped to here.

Leaving it on for multiple coats would certainly be easier, if that works well, but I have some doubts. I'm getting close to the varnish and paint stage myself, so I've been wondering about it also. I'm a bit worried about bits of tape getting stuck in the built-up dry paint, and/or leaving a thick ragged paint edge when the tape is finally removed. 

I wonder if a cleaner edge might result from varnishing the deck without masking at all, letting that dry well, and then masking for the first coat of paint only. The tape could be removed before the paint is completely dry. It might be possible to free-hand the edge of later coats without masking, once the initial paint edge has been established.

I'd like to hear from a few more guys out there who are experienced painters.    

I should mention a trick I have heard about for preventing paint from bleeding under masking tape edges. Here's a good description:

http://www.instructables.com/id/How-to-Paint-Clean-Lines/

It seems to me all the varnish coats should be done first, extending sliightly beyond the desired paint lines. The varnish coats could be feathered down by light sanding where they extend beyond the lines.

The rest of sequence might go something like this: Apply the masking tape to the well cleaned surface, and press the edge down firmly with a hard object. Brush a narrow light swath of varnish along the business edge of the tape, to seal it against paint bleeding. When that varnish is dry, apply the first layer of paint, and peel the masking tape off as soon as that feels dry to the touch.

At this point I feel inclined to just free-hand the edges of later paint coats without taping. Any better ideas? 

I too am nearing the paint stage of my Chesapeake 17 build. I have 2 more applications of varnish to the deck, and then I will prime and paint the hull and on to the deck about 1.5 inches. The paint will go over the varnish, as others have previously suggested.

My concern is also what happens when the masking tape  is pulled off. Clean or ragged edge. I know from previous house painting experience that it is best to remove tape while the paint is still wet. I plan on at least 2 coats of paint so the tape will have to remain until then. I bought the 'fine line tape' from CLC and plan to use that instead of blue or green masking tape. It does not allow paint or varnish to bleed through to the surface below, so I will not have to varnish the tape before I paint. I will do several mock ups to refine my technique. I know also that the method of removing the tape has a lot to do with how the finished paint job will look. Any more info or suggestions as to my plan will be appreciated.

By the way, this forum has been invaluable to me. This is my first kayak build. I have been here every day since December. Lots of info and links to a lot of great sites. Thanks to everyone and especially CLC for contributing this forum.

One thing I've learned about masking tape is to not remove it by pulling straight up on it.  That may pull the adjacent paint with it.  Pull it away from the paint by folding it back and away from the painted edge, sort of a horizontal pull.  Keep an eye on how it's progressing and be prepared to occasionally assist with a razor knife along the painted edge.