After renaming the original installation of CFS2 and it's desktop shortcut, you can install the next installation as you would an original. Renaming that one too, you can put in another and so on. Counting a clean, unmodified install, I have a total of 9 in my Microsoft Games folder and on my desktop.
To make a Mission Builder for each, open the main folder of any renamed install and make shortcut for the renamed CFS2.exe. Right click on the shortcut icon and select properties. Under the shortcut tab, under Target, change the ending from xxx\cfs2.exe to xxx\cfs2.exe" /BUILDER .