To tell the difference easily if it ever happens to you again, just open your Driver Station and go to Setup with the controller connected to the PC.
You'll see a drag&drop list of all the joysticks connected (if a joystick doesn't appear, just push a button on it and the list would refresh). The first joystick in the list is the one you set to "USB 1 port" in your code's Begin.vi, the second is USB 2 etc.
You'll also notice that a controller would only take one slot in said list, while your 2 older joysticks would take one slot
each. So, going by this logic, you'd need to use just one reference for the controller in LabVIEW like you said. Some joysticks and controllers (typically the vast majority of them other than Logitech Attack 3 or Xbox 360 controller) are completely messed up when it comes to axes/buttons ordering, you can either fix that by utilizing the appropriate drivers or making a small LabVIEW program with indicators for all the joystick's outputs and make a chart out of it.
Tip: In my experience, it's much easier to test your code with joysticks though, especially the ones that have winch/throttle axes as they're so flexible and you can assign certain tested variables to those extra axes and you get so many options with all these buttons on 2 joysticks. Plus, pulling the trigger feels MUCH more natural with a joystick to me when testing a shooting system, and the migration to a controller (in case the driver wants that) can be done very easily even without the robot between the end of the build season and the competition. But all in all it's your choice of course
