You can install the normal version of Waterfox, you don't need the portable version to separate the data.
Right-click the Waterfox shortcut, go to Properties and add a
-P on the end of the target. Then open the shortcut and it should open the profile manager. All of your personal settings and data are stored on profiles. You need to make a new one for Waterfox. Once you have made a new one (remember the name!), close Waterfox, right-click on the Waterfox icon again, go back to Properties and add the name of your profile to the end of the target in speech marks along with -no-remote. For example, now it should say something like:
-P "Waterfoxprofile" -no-remote (make sure you use your own profile name).
Do the exact same thing with your other Firefox shortcut (make sure you specify the name of the other profile, NOT the Waterfox one). Now you have two different shortcuts for two different browsers that each open their own browser with a different profile (which have different data).