Having someone on the 25 man roster means they are on your MLB team.
Being on the 40 man roster means that it is possible for a player to be on the MLB team. A player cannot possibly be on your MLB team without being on the 40 man.
Having a player on the 40 man has benefits and drawbacks. Obviously the first benefit is that it is possible for them to play in the MLB. The second is that they are protected from the rule 5 draft, a draft that happens in the off season where teams get a chance to take other teams players. Only players who have been playing professional baseball for a set amount of time without being on the 40 man qualify to be drafted. You can find a player's rule 5 draft qualification status on their player card, and the new phases feature will warn you if one or more of your players qualify before the draft happens. Players that are drafted in the rule 5 draft must spend the entire next season on the MLB (25 man) roster or else they are returned to the team that they got drafted away from.
The drawback is that once a player is on the 40 man roster, they get three options. Options allow a manager to send a player to the minors without consequence. Once an option is used, a player can be sent down and called up an infinite number of times that season without consequence. So three options basically means three years of free movement between MLB and the minors. Once all three options are used, a player must clear waivers before they can play in the minors (and not count towards your 25 man). This basically means that every other team has a chance to claim that player for a few days. Once a player has cleared waivers they can be called up or sent down until the next waiver reset, which happens a few times a season.
So in essence, you want to populate your 25 man with who you think are your best players, and your 40 man with people you think have a chance at playing in the MLB. You want to keep everyone else off the 40 man for as long as possible, until they either qualify for the rule 5 draft (if you want to keep them) or you feel they are MLB ready.
Sorry for the essay, I know English isn't your first language, let me know if it's too much and I'll try to edit it and simplify the wording.
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