Part1 - Computer:
1. Download Win2DS Fusion here: http://www.1emulation.com/forums/index.php?showtopic=27746
2. Port forward for port 8888
3. Run "Win2DS.exe" (from the download in step 1)
4. Run "Nintendo 64 (Basic).exe"
5. Open Project64 (Download if you don't have it)
6. Set the controls to deafault
7. Load up a game and press ESC to maximize

Part2 - NDS:
1. Start your ds and load Win2DS (from the download in Part1)
2. Enter your lan ip

3. Select custom keys and set them to:
F1       F6
F2       F7
F3       F8
F4       F9
F5       F10
Then press start.

4. Choose "Virtual desktop", then press start. Set zoomed screen to off, and full screen to ultra.
Set the cotrols to "use custom keys" then press start again

5. If PJ64 is open on your computer and in full screen, then you are ready to play!
Here are the controls:
DPad = Analog stick/DPad
L/R = L/R
Y = Start
X = Z
A = A
B = B

Hints:
.This may run smoother if you have a good internet connection and cpu

.The Win2DS settings i use are:
Frameskip - 0
JPEG Quality - 15%
Resize Filter - High
Alpha Blending - Off

.The sound does not come through to the DS, so if you want to play it away from the computer try using wireless headphones
.Use the DPad version for games like Kirby 64
.Use the Pokemon version for Stadium 1 and 2
.Press R first to play on the top screen, then use Black.png to make the bottom screen black