make sure you have not delegated that. go to manager's office -> manager control settings or similarly named page. there will be many check boxes that control things like minor league depth charts. make sure it's delegated. (if coach only, you can't do it, that i know of, unless coach of that particular team, of course.)
when you are on you own lineup screen, you can select the drop-down box at top of screen that says <insert your major league name here>. then, select an affilliate. they have their own section seperate from mlb teams (i.e. your equivalent ML level name).
you could change leagues first, then select lineup too. as long as you have at least 1 affiliate in that league, you'll go to 'your' team when you select lineups or pitching etc. even front office ("this level has no front office"
)
extra note: in settings look for a dropdown box in upper right area... can select leagues for various settings/options screens. "available actions" in similar area has lots of useful stuff too.