As you have noted the editing of a Site Sculptor site with CSS Menu Writer will cause the menu files to be overwritten. This is one reason we do not suggest using menu writer to update the menu on the completed site. 
When you look at your literature in the features section on Site sculptor it says "# Compatible with CSS Menu Writer
* Import a custom menu created with CSS Menu Writer
* Customize your menu further with CSS Menu Writer 2"
showthread.php?p=61819&posted=1#post61819
Sure can! There is a simple menu.php file that contains the unordered list that you can add any additional links to. For some more functionality when modifying the menu, you can use CSS Menu Writer. 


