Basically, the Header Builder v2 still keeps 3 rows: Header Top, Header Main and Header Bottom. But now it converts from 12 columns on each row to 3 columns: left, center and right.
To use the header builder v2, you just need to click the Switch Builder Version button and select Version 2.
At the bottom of the header builder editor, you’ll find builder elements that can be added into the header area. You can drag and drop the element into the header area you want.