I think there's a fundamental misunderstanding about the draft settings page that arose with the introduction of the formula builder. I know I've misunderstood it myself for my last 3 drafts.
You can use EITHER the player settings OR the formula builder, but NOT BOTH. THEY DON'T WORK TOGETHER - THEY'RE 2 DIFFERENT SYSTEMS. If you check the formula builder box on the draft settings page, it cancels anything you've done with the player settings.
The way this can become a real problem is this: there's no way in the formula builder to specify how many of WHICH POSITION you want to draft.
A lot of owners are filling out the player settings section AND using the formula builder, then wondering why they drafted 21 pitchers in a row (actually happened in the last Kinsella draft...another team drafted 18 pitchers in a row). Both these teams bumped up some of the pitcher ratings in the formula builder, seeking to move pitchers up in the rankings. They also thought that the player settings would keep them from "overdrafting" pitchers. What they didn't know is there WERE NO PLAYER SETTINGS.
To me, this just renders the formula builder useless. I've made the same mistake in all of my last 3 drafts and got unbalanced results (position vs. pitching) all 3 times - had to go running around trying to sign minors free agents and waiver guys just to fill the rookie teams.
By the way, I sent a ticket to WIS to confirm that I understand this correctly; but there is confirmation in the second paragraph of the draft settings page instructions:
"To generate your draft board, you have two options (both of which rely on your college and high school scouting departments): The simple approach to the left or the formula builder outlined below."