I took one of them out to see if it is rotten and it actually grew a big 2 cm long root.

Now to place it back I'll put the root down but will the seed have to be burried deep as it was before (about 2cm in the ground) or should I leave it nearer to the outside? Right now I placed it back and I can see the green plant outside and the seed is just beneath the soil, I can actually be seen a bit. Is this ok or should I plant it deeper?

Thank you,

leave it as it is .

Green part is the sprout or germ. Anyway, it should be facing upwards, and you should plant it right above the soil surface.