Hi - firstly thank you sincerely for all of the efforts in making this game.

Is there a way to alter conference memberships short of modifying the underlying database? Do conferences realign periodically "naturally" as the sim progresses through the years?

In between seasons you can manually adjust your conference alignments, either moving teams around or changing current makeup of conferences. It does not happen automatically, but time does affect conference prestige.

Thanks! Sorry for the dumb question - which screen do you use to do realignments?

It's in the upper left under options and then on the league format tab... but only in between seasons in the "begin new season" stage.