The Rules sub-screen (Game Menu >> Advanced section >> Setup and Options >> League Setup tab >> Rules tab) allows you to change the rules within your leagues. These settings are identical to the ones described during the game creation process.

Some rules, most notably financial ones, can be changed only during the offseason. Those rules will be grayed out unless it is the offseason. Specifically, you cannot enable or disable the overall financial system during the season, nor can you change free agency or salary arbitration settings.