You have to tell the Everdrive 64 to use the Dezaemon 3D SRAM emulation save type for the emulator.
To do this, open the file
save_db.txt which is in your SD card's \ED64\ folder.
And add the following lines to the bottom of the 'save_db.txt' file:
0x8979169C=4 (neon64 NES emulator v3 - Press L and R for savestates)
0x1974961C=4 (neon64 NES emulator v3 - Press L and R for savestates)
and it will probably work. It tells the Everdrive 64 to use the Dezaemon 3D SRAM save game method for two different versions of the emulator.
I can't test this, as I don't have my N64 with me, so it might be wrong. If this works, then please post to say so, and if it is wrong, then follow the tutorial:
https://krikzz.com/forum/index.php?topic=6125.0and please post here the right line to put into the
save_db.txt file.