this is what i have done, but like i said, it always boots in homebrew channel and i cant see the cia files i installed :
To clone the card
1) On your old SD, boot up Homebrew Launcher and open Emunand9 (From sysnand not emuNAND)
2) Go to "Emunand Manager Options", then choose "backup emunand to file". Choose a file name by pressing up or down on the Dpad, choose "emuNAND.bin" for the file name.
3) Once that's done, press B until you get to the main menu, go to "SD Format Options", then choose "Format SD (Emunand minisize)"
4) It will give you the option to switch SD cards before doing the reformat. Put in the new SD card that you plan to use with the 3DS.
5) Once that's done (Should take a second), press B to go back then press select to unmount the SD card. go to your pc and copy everything from the old card to the new card,
including emuNAND.bin. Be sure to place the emuNAND.bin file in the "Emunand9" folder on the root of your SD. This is where Emunand9 searches for emuNAND backups.
6) Put the new card back into your 3ds, go to "Emunand Manager Options" then choose "Restore file to RedNAND". Choose "EmuNAND.bin" and it will restore emuNAND.