Coach Parrot estimates that 2 position training is 75% of one position training. I can give two questions that may help you decide.
1. Do you want your players to reach their potential?
If yes, then you must train one position. It is difficult to cap a hall of famer even when training one position and two position training (aside from Jump Shot, One on One and Rebounding) makes it almost impossible. For lower potential players (e.g. allstar), 2 position is better for me unless you want him in U21.
2. Do you want your player to join the NT?
If yes, then you must train one position. For smaller countries, you might be able to get in even when training 2 positions but you will hurt your chances if you train 2 positions.
If your answer to both is no, then my opinion is 2 position training is better since it gives a higher amount of skill points overall. It is also better to switch to 2 position training when the players are older since the 25% difference is smaller. For example, an 18 year old receives roughly 0.6 vs 0.45 PA while a 24 year old receives 0.31 vs 0.23 PA. You lose 0.15 PA for an 18 year old while you lose only 0.08 PA for the 24 year old.