You only have to play 48 minutes to get the full benefit of training. But yes, do single position training. Doing multiple position training takes much longer, the only time I would ever recommend doing multi-position training is if you do not have a specific trainee who you are training. The OPs focus should be on training this player right now due to his age and potential, even at the cost of wins.
Training out of position will help in the long run, it also will allow you to be creative with tactics as your player develops. I have a SF I am training who had skills around 10 at nearly every skill, he was very valuable when I was at D4 because I could run odd lineups and switch up my tactics. This player would still be a productive player running look inside when I was training him at PG and motion or patient when he was at C. I still do this a bit at D3 (in my first season at D3), but it is not as effective. That said, I will be happy I trained him this way when he is a stud SF who is hopefully helping me get to D2 in a couple seasons.