The Minor Leagues screen (Team Menu >> Transaction section >> Minor Leagues) is where you can manage any minor leagues within the selected team's organization:

The Minor Leagues screen behaves very similarly to the Overview page, except that by default, the boxes for the top four minor leagues in your organization are displayed. As with that page, to make a transaction, drag a player from one pane to another, or right-click on a player and select a transaction from the right-click menu.

Note: This sub-screen is not available if the selected team does not have any affiliated minor league teams.

The Transaction Legend and Action Menus are both identical to those described on the Overview screen, as is the link to the Minor League System Report.