I'm certainly no expert, but I'll be facing this problem soon (building a Wood Duckling).

You might want to check out videos on Wood Duck/Shearwater build classes that Eric Schade (designer and manual author, I believe) recorded in years past.

https://www.youtube.com/watch?v=Tdq8rE4WfhM (spring 2013 or earlier?)

https://www.youtube.com/watch?v=vsw7e1VqQeo (fall 2013)

https://www.youtube.com/watch?v=nNPz3wjlPAQ (fall 2014)

Naturally, I suddenly became very curious about the content of those videos after linking them and quickly discovered that there is nothing insightful about glassing the transom there (as far as I can tell).

I did check out each of the three build blogs I've bookmarked, though, and I noticed that vupilot had a few notes about glassing the hull (in particular, the transom) in his March 17 entry:

https://woodduckkayak.blogspot.com/2011/03/ 

There is nothing insightful because it's no big deal. The transom is flat, the edges are well-defined. You don't need darts or bias-cuts or anything like that. I honestly don't remember how I did it, it was that easy (and 13 years ago).

I think I put a flat piece of glass onto the transom and then overlapped it with the hull glass. Or it may have been the hull glass first and then the flat piece. Either way, it's easy to apply and with careful feathering the seams are totally invisible, which is why looking at it just now I couldn't see what I did.

So be happy, don't worry, it's not a big deal.

Laszlo

   I just finished glassing my wood duck 14 within the last week. Both the hull and deck are done, and by far the deck was one of the most difficult parts of this build. That being said, I will 100% admit that it was probably my own doing. My advice, unsolicited as it may be, is to mix small batches, lay out your glass well in advance, make sure it is smooth, and make sure you are drawing away from the center or towards the ends/edges. Take your time in advance so you can be efficient and effective during the pour. Lay out the glass and run your hands over it to smooth the wrinkles, use a chip brush, whatever works, just get the wrinkles out. As for the transom I tip my hat to Laszlo, I didn't even think about just laying a flat piece on, I just cut a "V" and overlapped the edges.