Thanks again for your help! Knowing this is a relatively complicated game, and adding in the sandbox aspect, I spent a fair bit of time reading the manual and the forums before even buying it; figuring that I should at least have a basic understanding of what the game can do before I spend 40 dollars and lots of time on something that may simply be over my head.
But then I saw how much people help each other on the forums, and that was one factor that made the decision for me
Basically, I started a few different universes, and then realized I had this or that setting wrong (like inflating the number of amateur rounds more than I should have), or did something stupid to mess up what I want to do.
Basically, what I'd really like to accomplish is start with the MLB setup, with a AAA, AA, A, and Rookie League, delete the previous history (to take away the difference in eras), run the league without my involvement for long enough, maybe 50 years or so, to set a baseline for standout performances/careers/teams in which everything is relatively equal (era-wise) but similar to how things are in RL (like market size/budget differentials).
Then, expand the league with a team in my hometown, which would make it a small-market team. I'd like to run that expansion team and see how my team/players perform over the same period of time -- 50 years or so -- compared to how the game ran its teams during both the pre-expansion and post-expansion mini-eras.
It might be a dumb way to set it up; but that's what I've wanted past baseball video games to be able to do since way back when; and now it seems that OOTP has just the game

Now it's just a matter of me figuring out how to shape the sandbox to fit what I want to do; and without turning every player into "Smith Smith".