Yes, it's possible to run RocketDock on multiple instances, but you have to do some tweaking first.
Download the application from the official website: http://files.punklabs.com/RocketDock/RocketDock-v1.3.5.exe
Install it, and then copy the entire folder another location, but before that, access the settings of the software. Customize it and check the Store settings in a INI file. Copy the folder to another place, and uninstall it.
Then, copy the folder again and rename it (for example, C:\RocketDock_UP). Run RocketDock.exe and change the settings. Close the dock and make sure that a file "Settings.ini" was created in the directory from where you've launched it.
If you want to place it in another location, create another folder, copy the contents and run it again, but access the Settings.INI with Notepad and modify the Side to where you want it. Write 1 to enable and 0 to disable.