Yes, exactly. You can also rename one of them to something more permanent by using the Target > Configuration > USB option in MFDeploy.
For instance, you could name one "NetduinoPlus_PeanutButter" and the other "NetduinoPlus_Jelly". [Bonus: if they ever become sentient, they'll already be friends...]
Naming them is probably the best option...because them it won't matter which order they're plugged in...Visual Studio will always recognize them by their custom names.
Chris
Excellent. Thanks again, Chris.