I had to figure this out the hard way so I figured I'd post for others so they can quickly find the solution. I use my ps3 controller for my controller and don't wan't to reach forward all the time to hit the mouse. I simply download joytokey, @ joytokey.net, open zip file, open folder, open JoyToKey.exe. Double click each button you wish to use as your mouse (such as stick 1 <-) select the "mouse" tab and under "mouse emulation", "cursor movement", you will move the tab in the direction you wish to move  mouse with said button (EX: double click "stick 1 <-", "mouse", move horizontal tab to far left, then select "OK" at bottom of window. continue for all directions) NOTE: to adjust speed only move the tab the percentage of speed at which you wish the mouse to move (I'd only go 40 on each direction). Then select a key to use as your mouse input, for stylus you just need the "left click", double click your button of choice, select "mouse" tab, check "left" under "mouse click" then click "OK". After your analog is set as your mouse start desmume and make sure you do not assign any desmume keys to your stylus analog. Done.

Things to note: Firstly, analogs sticks are hard to use as the stylus for fast paced games like TWEWY and legend of zelda. Adjusting the speed of each analog direction will help but it's still difficult.
Second, for those unable to assign the right stick, select "Settings", "Configure Joystick Devices", "Advanced settings for each device", "Axis mapping" with 2 dots appears, move stick in question, if dot doesn't move but side bars do just adjust the horizontal and vertical axis' beneath the dot that you want to move, to "X axis" and "Y axis" for "stick 1", and "Z axis" and "RZ axis" for "stick 2".
  And Finally, joytokey must be on for it to work.

Hope this helps. Direct questions to JoyToKey as that's all I know lol ^^'