having trouble aligning the top menu
 

http://www.scagliola.biz/

I've moved the menu to the side but I'm having problems with the top menu dropping down - I had to add some padding to the Overall Style & Config./Body Style to make the text drop down and not hide behind the lower menu bar at the top.

And, it all sort of jumps around when you change pages.

Any ideas what I can do to fix it?

The Atahualpa "style" you are using has the background image of the gray bars and has to be dealt with by editing or position the menu with CSS. Take a look in ATO>Export/Import setting for information on those styles but be aware if you import one it will overwrite you current setting so you should export what you currently have first.

Because of that background image you will have to fiddle with perhaps the height of #container or perhaps the logo area styling in ATO>Style & edit Header Area