Here's all the settings for the Header area of my theme (my theme is based on the no longer in use Jupiter theme which has been altered in images and in positioning via CSS quite a bit)
Header Properties:
Header Area Background - Transparent
empty
no repeat
nothing set on Horiz or Vert position and both at 0
Header Background - Transparent
empty
no repeat
nothing set on Horiz or Vert position and both at 0
Shop Logo
image file is pointed to here
Keep Original Size is checked, and image is sized according to site area wanting to be covered
No borders
Hide Text
Shrink Header area - unchecked
(these settings may need adjusting according to the theme you are using, these are what work for Jupiter Theme setup)
Header Margins
28, 220, 0, 37
Header Padding
5 all across the board
Header Text Margin
74 all across the board