Ok. It's basically all in the manual page but anyway... (I'm on windows)
1. Decrypt you rom (I'm using Pokemon Y) - You should already have this done previously i guess.
2. Download the zip from layeredFS github
3. Copy the
exefs.bin from your decrypted rom to the
workdir in the layeredFS folder.
4. Double click the
build_layeredfs.bat, when it asks for the folder of the layeredFS... enter it, for eg i have:
layeredFS/0004000000055E00 (i made a folder on my3ds sdcard called layeredFS then another folder inside that called 0004000000055E00), press enter, then enter again to close the window.
5. If not already done so, make those folders on your 3ds sdcard, so from the sd root it will look like this...
6. Now in that last folder make a folder called
a then copy the folders from inside the manual installation folder from Pokemon Neo XY (full or lite, your choice), i did full so the folder looks like this...
7. Create another folder on the sd root called
plugin then another folder inside that
0004000000055E00
8. Copy the
layeredfs.plg you created earlier from the
workdir of layeredFS to the folder created in step 7.
9. If all went right the top screen will flash green for a second when the game is started which means the plugin is working.
10. Hope this was helpful