I have not used rocketdock for a while but they did used to have an option to store all settings in an INI file rather than the registry.
if this option is still valid it should be possible to install the application to two different locations, and call each separately, as the settings would be independent, each could be set-up to appear in two separate edges of the screen.
Note
Due to the way that RocketDock saves the INI files to the Program files area and the security of Windows 7, you will need to take ownership and full control of the application directories