There are three parts to the Neo Myth 3 in 1 cart for the MD: the Windows client, the plug-in for the Windows menu, and the MD menu. At points, the latest of all three are collected together in the Windows app installer, but at the moment, you need to get all three separately. The posts they can be downloaded from are linked here for convenience.
The current client for writing flash cards from the PC is the Neo2 Pro Manager v1.20. This should be used unless you run into trouble.
The old PC client is Neo2 Ultra Menu v3.04. This supports the MD Myth, N64 Myth, SNES Myth, as well as GBA/NDS flash cards in general.
The current plug-in is v2.2.0.3. I'm not aware of any problems with it at the moment. This should be copied into the Plugins/MD directory.
The current MD menu is v1.2b1. It should be copied into the main Neo Myth directory. It will replace the MDBIOS.BIN file already there. When you change this file, run the Windows menu, go to the Format tab and do a fast format.
The current deluxe MD menu is v2.5. We recommend you use the deluxe menu. To use the deluxe menu with Neo2 Ultra Menu, replace the MDBIOS.BIN file in the Neo2 Ultra Menu directory with the MDBIOS.BIN from the directory (not the MDEBIOS.BIN file!). Go to the Memory tab and click MENU Write. Set the size to 4 Mb, select the MDBIOS.BIN file and click Write. Then go to the Format tab - set the menu flash to fast format, and the game flash to standard format. Make sure it is set to do a MD 3 in 1 format and click Format. After it's done (a standard format can take a while), you are ready to add roms like normal. To use it with the Neo2 Pro Manager, copy MDBIOS.BIN over the existing file in the folder in Program Files; then click Burn and it will check the version of the menu on the flash against the file on the harddrive and update it if needed.
Neo2 Pro ManagerWindows menu clientPlug-inMD Deluxe MenuMD Menu