inovative use of soda cans there, lol

the roots will grow down by themselves, planting too deep will just encorage the grow top to rot.
once ive got fermination, i barely even plant them, i put them right on top just deep enough for the tap root to dig in....ive never had a faliure yet.
see pic.

dunno what to suggest about that leaf, try ditching the heat pad, you dont realy need it indoors, and it may be contributing to the rotting problem that looks like that leaf?