Minor Leagues: How to Use
 

If I start a sim from 1901, how does minor leagues get reflected all the way through 2006? If you only start with X major league teams and X minor league teams, do additional minor league teams get added as the league expands? And if so, how do they get assigned as affiliates?

Each major league teams gets one auto-assigned affiliate at each level. As there are fictional when expansion expands the minors expand expansionally as well. The game assigns the new minor teams as it sees fit. One per level per new expansion team.

Is there a way to import real minor league affiliates into a historical sim? I started a 2006 historical sim with Lahman database and I'd like to use real minor league teams (don't care about players). Am I supposed to use a template or something?

In theory you should be able to create the minor leagues as templates, and then when you make your historical sim, (2006 isn't much in the way of historical, but whatever) load the minor leagues from templates.

However, you may have to sim a day or a year (!) to affiliate the leagues with the majors. Actually, it's not too bad since the minor leagues didn't affiliate with MLB until after 1920....