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,
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,
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.
D Pad can be KEYS or POV. POV will automatically choose a continuous or 4 directional POV hat depending on what is set in your vJoy Config. KEYS will allow Left, Right and etc. to be buttons as previously.
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, WINDOWS, ESCAPE, CONTROL or ALT), or a joypad button (JOY1, JOY2, JOY3, to JOY16).
