The first thing I would recommend would be to download both programs and see how you like them to decide on one. Then use it for a while to see what controls you use typically.
I found with VMJ that I could do about everything with a right and left arrow, a keypad and 4 "group" buttons. I use the * and # buttons for skip and random.
The above switches would interface to you computer via a keyboard encoder which your computer just sees as a normal keyboard. I would recommend going to the main site and reading through the pages on arcade controls since they are essentially the same thing.
Hope this helps!