If you mean as part of your initial setup... see below.
When you set up your league... click on add feeder league.
Then in the lower left of the page (where it shows your entire universe... Major League, AAA, AA, college feeder, etc) click on the feeder league so it is the active league that you can now change the options on.
Go to League Structure see link
OOTP Baseball Manual - League Settings
It looks just like the link above except where it says Major League Level in the screenshot it should say your feeder league in game.
Change the # of teams in the dropdowns.
If it's after a season or two... I think you have to wait until the offseason.