I personally keep all my docks in one place...in the above mentioned folder...and have no plans on creating multiple background.ini's or duplicate docks for each of these new folders...to much "work" involved.
For me i still don't understand what's the use of the E:\Mes Documents\ObjectDock Library (hehe, because My Documents is in my case not stored on C:\ but on E:\

) and though apart that themes.ini are stored in E:\Mes Documents\ObjectDock Library\Backed Up Themes and no more in C:\Program Files\Stardock\ObjectDock\Themes (

) the other subfolders don't have any use for me ...
I'm the third to don't like these extra folders as well ...