If you installed Cordova, then you'll always use the cordova command. When you do this in the terminal ...
cordova plugin add org.apache.cordova.geolocation
... it looks for a hidden folder called "cordova," so if you typed "phonegap" or something other than "cordova," then the command won't work. So if a project calls for you to type "adb" as the first word, it is assuming you've already changed the directory to the folder that has the "adb" folder in it.
The second word is giving the command to execute that's inside the cordova folder. The following words seem to be the arguments so the command knows exactly how to carry out the order.
I hope this mini-tutorial on terminal commands helps you understand how to differentiate between cordova and phonegap usage.
You'll download and use "phonegap" if you want to use the PhoneGap Build service. If not, download and use "cordova." If you want to use phonegap, then just open a new folder separate from the cordova project and download phonegap into that, then copy the files over, installing all the plugins again. (I'm pretty sure this is how it's done.)