Been a long time since I did autodrafts but i used to do them all the time. Yeh, Yahoo will fill your starting slots before doing bench positions so in theory you could put 30 RB's first and you'll only get RB's with your first 2 picks and it won't come back to the top of your list again until the other slots are filled. I used to have different formulas worked out that worked pretty good but I can't remember any of them it's been so long.
What you might want to do before you draft in your league is to draft in a public league for practice to see how it turns out - just don't abandon your team after ya draft, stay active.
The biggest drawback to an autodraft is you can end up with 2 TE's, 2 K's, and 2 D's (sometimes ya just end up with doubles in two of these), so you're gonna wanna get rid of the doubles and pickup good backup RB's and WR's right after the draft as there will be good ones left - if you're not sure who to grab, the Cafe is the place to ask.
Any other questions, ask away!