What is the CSS Sculptor Preset that you choose originally? Please post back with this info and also some info about the steps you took to implement the layout.
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.