I did a test like you described of checking the top navigation box in the interface, I then saved this preset as new Sculptor layout.
Once saved I used the preset manager to create a new SiteAssist Pro preset, I choose the sculptor preset that I had just created and also a menu that I had created. I put the menu in this top navigation section and just set the other areas accordingly.
When I generated a new site based on this I was able to see the navigation just where I had specified within the top navigation area.
i have chosen 3 column, fixed header and footer
I have changed the pagewidth to 900 pix, checked the 'topnavigation check' and inserted a menu with Menuwrighter.
After all this i have saved the page as a dreamweaver_template. Than from the preset manager i have chosen 'new' and checked the dreamweaver template i just created. further i have chosen in the presetmanager in the poduct-tab Siteassistpro layouts. Than i have passed through the 4 steps (in my case step 3 and 4 are exactly the same as 1 and 2 so that makes no sence to me)
When i do not check teh topnavigation check and create my own navigationdiv the problem does not appear.
Important: i work on a Mac
Eric, im my opinion there is no clear description or any other solutionrecipe that explanes this matter systematic. (i mean how to use the presetmanager to handle sclulptor laypouts or DWT's) When i am wrong please tell me where i can find this.