Notice: this information was written when Microthemer version 2 was current. On Dec 26th, 2014 version 3 was released with a completely new interface. Some of the information may be redundant, but as much of
the functionality remains the same in version 3 we haven't deleted this post.
I may just modify the main twenty eleven theme to accommodate this by wrapping the two divs in a main div. I am currently using the div before to show the graphical background header.
I’m not entirely sure what your objective is here. From inspecting the divs with firebug it seems that overlapping behaviour of the #primary and #secondary div is caused by left and right floating and a negative right-margin on the primary div.
Perhaps a link to the site your currently working on with some more specific instructions would help me assist you further.
If so, I think you could try adding the background image to the #main div instead of the #primary div. In order for this to work you will need to set “overflow” to “hidden” on the #main div (otherwise it will have no height because both #primary and #secondary are floating).
