Initial Setup of an SD Card

First steps

Connect the SD card to your PC and ensure it is properly formatted to be compatible with your flashcart.
WARNING: Filenames are expected to be written in ASCII, with Western Europe characters fully compatible. Other Unicode characters, such as those from Eastern Europe, Russia, Asia or Middle East regions (to name just a few examples) are not fully supported and may not be displayed.

Note: It is advised to use ROM files in the Big Endian (default, also called "non-byteswapped") format. Although the menu auto-converts byteswapped ROM files, the load time will increase.

Preparations for SC64

FAT32 and EXFAT are fully supported.
An SD formatted with 128 kiB cluster size is recommended.
Download the latest sc64menu.n64 file from the releases page, then put it in the root directory of your SD card.
Place your ROM files on the SD card, in any folder except menu. NOTE: byteswapped ROM's will increase load times.

Preparations for other supported flashcarts

FAT32 recommended.
An SD formatted with the default cluster size is recommended.
Download the latest menu file specific for your flashcart and place it in the expected location.

Emulator support

See the Emulators page.

64DD Disk support

See the 64DD page.

So what would the layout of the SD card look like?

SD:\
│
├── sc64menu.n64
│
│
├── menu\
│   │
│   │
│   ├── 64ddipl\
│   │    ├── NDDE0.n64
│   │    ├── NDDJ2.n64
│   │    └── NDXJ0.n64
│   │    
│   └── emulators\
│        ├── neon64bu.rom
│        ├── sodium64.z64
│        ├── gb.v64
│        ├── gbc.v64
│        ├── smsPlus64.z64
│        └── Press-F.z64
│
├── (a rom).z64
├── (a rom).n64
├── (some folder with ROMs)\
        │   └── (some folder with ROMs)\
        |       └── (some supported ROM files)
        │
        ├── (some supported ROM files)
        |
        └── (some folder with 64DD disk images)\
            └── (some 64DD disk images)

Save Files

All save files (whether FlashRam, SRAM or EEPROM) will be read from a /saves folder located in the same directory as the ROM and they must share the same file name, but use the .sav extension. .sav files will be created and modified whenever a ROM file saves to the "cartridge save memory".

├── (some folder with ROMs)\
    ├── a_rom.z64
    ├── b_rom_whatever.n64
    └── saves\
        ├── a_rom.sav
        └── b_rom_whatever.sav

Transferring saves from an ED64

If you are transferring a file from a different flashcart, such as the ED64, you must change the file extension to sav. For example, a save file called Glover (USA).eep should have its extension changed to Glover (USA).sav to work with N64FlashcartMenu.

You may also need to pad/trim the files to their original size:

For EEPROM 4Kbit games, remove the padding.
For others, use a tool such as Ninjiteu's N64SaveConverter.

WARNING: Saves created with certain emulators, or created for a different ROM version (as in revisions of the same game) or region (as in between NTSC and PAL versions of a same game) may be incompatible.