Can a sidebar span two zones in omega 3 theme?
No, with the way the HTML is built, it goes


zone-wrapper div (if used)

zone dov



region div




In your case, I would leave the Header zone empty (make sure the checkbox for forced rendering is off), and then move all of your regions to the Content zone.  In the grand scheme of things, there is nothing special about the Header zone.  I am looking at one of my sites now, and I left Header empty.

With the default templates, the Content zone also contains the Breadcrumb and Messages, so you may need to tweak this a bit to output the regions specifically to get these in the proper place.