I would like to see the study plans of your design. I also designed one using the KayakFoundry. I'm 9 strips up on each side. I haven't had any problems that could be attributed to the KayakFoundry. Ross's program did exactly what I told it to. My problem was a little more cancavity near the stern than I wanted. Since, in the past, I've primarily been a by the eye and batten builder my problem was a result of inexperience in using drawn plans and my interpretation of some of the contour lines. The program clearly showed what was going to happen. Very minor reshaping of the stern and bow form and eliminating form #14 took care of the problem. I have also experimented a little more with the KayakFoundry and found that I will be able to design a wineglass stern kayak with it. It will be an interesting project for the future. I'll probably post more pictures of the current kayak within a week.
As for hatches...I just put them where they look good and where I want them.