[1998 Yankees]

You could make a human manager identity for each team and seize control of each team in the organization (must be the commissioner temporarily to do so). This would put you actually in charge of the teams, bringing benefits that don't occur with the alternative below. However, it would be pretty time-consuming, having to sign out of one ID and into another and switching between league levels, and each manager identity would have to be set correctly as far as team controls.

You could also take on commissioner powers which among other things would allow you to manage in any game you want, at any level. This would save time but being commissioner is not the same as being in charge of a team, as you would discover. For example, you don't get certain notifications as commissioner unless you actually are in charge of a team.

Either way, it would be very important to set Simulate World in Background to "No" in Game Options (just before you play out a game) because if that says "Yes" and you played one game that day, all the others would be playing in the background, I believe. The setting is sticky; set once, future games will retain the same option.

Edit: On second thought, the best option may be just to play in commissioner mode. That way, you can be the GM of your organization, playing out your MLB game then switching to each league level to play out your affiliate games. Just don't forget about that Simulate World in Background thing.