I'm running a few drupal based sites within the same account at Green Geeks. The way it works is that one site is the primary at the root and the other sites are located in sub directories below the same root. For some reason I wasn't able to drag and drop the blocks in the Administration->Structure->Blocks section to rearrange the different blocks, but it was working well for the main site. To get it to work I did the following.
The next (and final) step is to edit the .htaccess file in the sites in the sub-directories. All that's needed is to comment out the last section between the <IfModule mod_headers.c> ... </IfModule>HTTP:Accept-encoding and Header append Content-Encoding gzip pieces are. I believe that this stuff is doubling up the same options from the master directory a level below.
That made the dragging and dropping of blocks work for me.