@saween,
I hope this helps, here is what my set up looks like:
in /recalbox/share/roms/daphne
[ls -l]
lair2.daphne
in /recalbox/share/roms/daphne/lair2.daphne
[ls -l]
I have all my .dat, .ogg, .m2v files and:
lair2.commands
lair2.txt
lair2.m2v
lair2.ogg
lair2.dat
all the other files start with dl2-XXXX.dat, dl2-XXXX.m2v, dl2-XXXX.ogg
where XXXX is some number
In /recalbox/share/roms/daphne/roms
[ls -l]
lair2.zip
Notice every lair2 file (lair.zip, lair2.commands, lair2.txt, lair2.daphne) are all exactly the same (all lowercase)