I am running windows 10 pro 64 bit and have two M-audio code 61 keyboards connected to the computer via usb.
 
Two issues:
1) Sonar X3 studio shows both keyboards but they have the same name displayed - it would be nice to change their names ...
2) In preferences: choosing both Friendly Name devices: Code 61, I get an error that the device is already in use... but Sonar X3 is the only software running.  is it some windows device that is causing this??
Thanks
 

I would use the USB connection for one controller and the MIDI ( DIN) connection for the other. I really can't see how windows or Sonar could ever separate the USB driver ID  of the exact same controllers. That ain't going to happen.  
The USB will always be the ID of that USB midi driver for that controller.
But the 5 pin MIDI ports will be associated with your Audio/ MIDI interface so no problem. 

You could try having one connected at startup, rename it with a friendly name, then connect the other one and see what happens.  Maybe then you can give it another name.
 
But why would you need 2 (unless you are playing with SONAR live)?

Hi. IIRC Bitflipper (Dave) had such an issue when "starting fresh" again a couple of years ago.
I think he ended up getting another kind/brand of controller, as Windows/SONAR couldn't "tell them apart".
I'll share the link if I find it, or even better if Dave comes by and tells it himself.
All the best.

Windows can, Sonar not.
I have tried to "rename" ports on Windows level. Theoretically possible. Practically not worse the result.