I did mine flush and it looks fine.  I could sand the edge of the seat so that it was perfectly flush to the bulkheads.  In my case I don't think I could have made the bulkheads fit the sides and leave much overhang in the seat.  My Skerry is designed with a lot of overhang and some curve to the overhang and also looks real nice so I think you could go either way as far as looks.  I do not think you need the extra fillet for strength so just go with whatever works for you.

Mine had a little natural overhang, about 1/2 inch, and I liked the look so I kept it that way, front and rear. It think it adds a little interest to and otherwise uninteresting joint.

Mine also had a bit of a natural overhang and i chose to leave it so.  It gives a bit of a shadow line and a little more interest.

I got a piece of 3/8 inch mahogany three feet long and used my tablesaw to rip long strips approximately 3/8 by 3/8 (a little thicker so I could sand down flush to the seats) and epoxied these strips to the thwarts and seats.  Before epoxying to the seats, I cut off a like amount from the seats, but left the thwarts as is and just added the extra 3/8 on both sides.  I could not really see leaving the endgrain of the plywood on the seats and thwarts and I think the strips of mahogany really look nice.  I left a bit of an overhang on the seats for the shadow line as indicated above. 

 Almost finished now!

That last reply was made by me and not JayC.  I think I timed out before actually hitting post message. 

Tim in Port Orchard

Thanks for the replies!

After shaping the seats, I seem to have about 3/8 inch overhang so I think I am going to go for the slight overhang. The shadow line/ interest idea sounds "interesting" :-)

Thanks for the support once again!

Tandy,

Sounds like a very interesting treatment. Can we wee some pics? 

Okay.  This is my first attempt at posting a link to pictures.  It has taken me a few days , but hopefully it will work. 

 This is the mahogany strips added to the seats and thwarts after 2 coats of epoxy, prior to sanding.

I hope this works.

Tim

http://picasaweb.google.com/114154163321583891694/BoatBuild?authkey=Gv1sRgCLTQ0MbJhYCC2QE#5455390050544043522

Thanks for taking the time to post pics. I like the look. I thought about doing something similar when I was building but my patience (or lack thereof) got the best of me. Nice work.