How do I get the most out of the draft? I see the great projected numbers in the reports and try to adjust my preferences accordingly but my guys seem to still draft whomever they want.

Draft settings.    Pick a few specific positions but have the vast majority set at "any".   That way it will take the first player off your list rather than the first SS(or whatever).

Go 'aggressive' or 'very aggressive'.

I'd rank the guys on my own rather then using a formula.

Here is how I do my draft board.
1) Best guys first regardless of if they are a pitcher or position player and regardless of if I think I am going to get them or not. Usually pretty easy to see these guys.

2) probably won't sign and DH get bumped past 100 on my draft board. I'm in the NL. No need for either.
3) guys that could be everyday players either SP, closers or everyday field players.
4) bench guys. Good defensive ratings and/or good base running. Setup guys get listed here too.
5) defensive catchers. Arm strength, accuracy and PC potential all over 70.
6) guys who can hit for power. All potential over 80.

Should get you between 30/70 guys ranked and you'll get between your first 4-7 picks from your list which is all that really matters.

The rating threshold should be?

none