i know options are limited in D3 with setting your lineup but is there a way to set your 3-4 defense up with putting the highest rated players in the right position? (i know confusing)
if i have a guy that is a better dt than de, how would i make sure he is playing dt?
same thing with cb and s and ilb and olb?

DB1 = CB1
DB2 = CB2
DB3 = FS
DB4 = SS

LB1 = LOLB
LB2 = ROLB
LB3 = LILB
LB4 = RILB

DL1 = LDE
DL2 = RDE
DL3 = NT

You can set your depth chart up to match this. However, when the subs come in, this will get all out of whack. Good luck and I hope this helps.

ps
This is if you are looking at the 3-4 formation on the page. Real life would be different on R and L

I would just put the players in order of their quality .
There are things that might vary that for me: Their potential(if one of them is lousy but has higher numbers I would probably put a High Potential guy there to grow), Their WE(same reasoning as Potential).