I can't get the grey bars to line up with the menu
 

The gray bars that span the whole width are a combination of background color on the menu bars and a background image. The background image is called in ATO>Body, Text & Links and can be tweaked to line them up or you can adjust the CSS for the menu bars to line them up.

Alternatively you could do the following.

• Delete the background image in ATO>Body, Text & Links for a new look and feel.
• Import a new style per these instructions which are in the FAQ thread. (Be sure to first export your current style so you can restore you current look if so desired).