This sort of ticked me off, since it isn't logical and it has never been explained this way, but the Commish told me this regarding whom the ROBOT chooses to pitch.

In the preferences section where you set starter, closer, MR, LR, etc., you can set anyone wherever you want them, and the robot will use them that way - with one major (and undocumented) exception.
In my example, I have Al Levine on a team. The computer defines him as a short reliever based on his MLB usage. Fine. But he's started games, and can thus be used as such in PB.
In my preferences, I set him in my rotation for the week. I have Joey Hamilton (defined as a starter by the game, but he sucks so I don't let him) set as my LR.
I, like any logical person, expect Levine to get the start when it's his turn.
As it turns out, REGARDLESS of whether you call Levine a starter, you MUST set your lineup and specifically click on Levine to start that game.
The ROBOT will otherwise select the highest rated (by PB value) starter as it is listed on the team page. Even if you define that player NOT to be a starter.
It makes NO difference that you have set a preference (much like the 3-years-running PH setting joke), the ROBOT will take what IT has defined as a starter unless you fully specify the lineup for a particular game.

Just something that needs to be better defined in the rule book....