Yes, you can have a Mission Builder for each installation.
For example, if you have a CFS2 installation called CFS2_BOB the shortcut for it might read like this:
"C:\Program Files\Microsoft Games\CFS2_BOB\cfs2.exe".
To create a Mission Builder shortcut simply copy the shortcut and change the Target in the properties to read:
"C:\Program Files\Microsoft Games\CFS2_BOB\cfs2.exe" /BUILDER: As you can see, it is adding the tag [space]/BUILDER: to the game shortcut that creates the MB shortcut.
You can then change the icons for each entry to be more recognizable on your Desktop or Start menu.