In short, all starting roster positions must be filled before the computer picks bench players. Therefore, if you already have your top 2 running backs picked and say you still needed a wide receiver and a QB- even if you still have a highly rated 3rd RB available and ahead of any available WRs and Qbs on your draft list, the computer will pick the WR or QB first. As to the question of which one (WR or QB) the computer picks for you, your draft list will determine which starting position will be picked (e.g. if you rank an available QB higher than an available WR, the computer will pick the QB first).

Below is what Yahoo says about your question, BDD.

When you are unable to draft for yourself, our computer system will make intelligent choices for you. This will happen if you signed up for an Autopick League or are not present for all or part of your Live Draft.

The autopick system first selects the highest-rated available player (based first on your pre-rankings and then our default rankings) that can fill one of the open starting positions on your roster.

After all of your starting positions are filled, the system determines a list of bench positions based on the number of starters at a position vs. the overall roster size. The system then selects the highest-rated available player (based first on your pre-rankings and then our default rankings) that can play one of the bench positions.

Given this system, it is important to remember that all starting positions are filled before any bench players are chosen. Additionally, keep in mind that the system will determine a maximum number of players to draft per position (starters plus bench) so that no roster ends up with an inordinate number of players at any single position (e.g., five quarterbacks in a league that has a single starting quarterback).

Regardless of your league type, it is wise for all managers to pre-rank players in case they miss any part of the draft. To do this, just go to your team page and select Edit Pre-Rankings.