If you have a custom schedule with interleague play created outside the game you can import it and use that.
You could also rearrange the league sizes and alignments in your minors so that an existing schedule file can be used. For example, the actual Pacific Coast League schedule file could be used if you have to 16-team league split into two 8-team subleagues and playing a 144-game season.
It depends on how many leagues you want in your minors to handle the number of teams you have. In the real world, there tend to be more minor leagues to handle the same amount of teams as compared to the major leagues. For example, there are 30 teams at the AA level but they are split amongst three leagues (Eastern, Southern, and Texas).
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