Mouse Speed controls how fast the Circle Pad or Touch Screen moves the mouse. If set to 0 and using the Touch Screen, it will set to the absolute position, rather than moving relatively to last position,
Buttons can be a letter for a keyboard key (like Q, W, E, R, T, or Y), a special keyboard key (like SPACE, CLICK, RIGHT CLICK, ENTER, BACKSPACE, SHIFT, TAB, LEFT, RIGHT, UP, DOWN, PAGE UP, PAGE DOWN, or WINDOWS), or a joypad button (JOY1, JOY2, JOY3, to JOY16).
If you want to use JOY9 through JOY16 you need to reconfigure vJoy. Search for vJoyConf in your start menu and set buttons to 16.
Throttle controls the delay between checking for new packets (in milliseconds), a high number will have slightly more lag between pressing a button on the 3DS and receiving it on the PC, however will make the application use less CPU. In my experience, 20 is a reasonable throttling amount,
vJoy Device chooses which device to connect to. Set this to 2 in a second instance of 3DSController to use a second 3DS at the same time, perhaps for multiplayer.