Stamina is hard since you probably have wide variation in stamina, so you may have to decide whether to not do skill training in order that a few players with low stamina catch up, while it may be wasted on other players.
It is sometimes hard to get enough minutes for training players who have low stamina, because the coach will keep taking them out of games. And it may hurt your overall performance, since starters who have lower stamina may play worse, or be subbed by players who aren't as good. There are a couple of weeks per season where there are only two games, so these might be better for stamina training. Also at the start of the season there are cup games, so you might want to use your best players more (to win) and won't be able to get training minutes for a lot of players.
You can always change your training up until the update on Friday, so if your minutes aren't working out - and they won't always - you can switch that week.
Starting out, I'd want everyone up to at least inept stamina, and then gauge whether some of your starters could use some more - and then do stamina training from time to time.