If you put the N64 menu in the U2 flash and the MD menu in the Neo2-Pro menu flash, you can use the same Neo2-Pro for both MD and N64 Myth carts. I'm not sure if the manager can put games in the flash for both systems... probably not, but you can run both off the same SD card; just put MD games in one directory, and N64 games in another... or mix them all in the same directory, it doesn't matter. It's just easier to separate them.
If you do this, be sure to set the N64 Myth to boot from boot path A2 (the U2 flash), and to set boot path A1 to the MD menu.