Lay out your string lines with "batter boards". At each corner of the building, drive three stakes about 2 feet away from the corner. The three stakes should form an "L". Nail two 1 x 3's or 1 x 4's across the top of the stakes to create the "L". Now you have a 2 foot range of adjustment for your strings. This will allow you to square your lines perfectly by adjusting the diagonals as others have mentioned.
I did this for a living several years ago (more than I care to count). We always set our poles 1-1/2" inside the string. Then when the girts were nailed on, the framing dimension was the building dimension. If you set your poles to be at the string, a pole that leans against the string slightly will push the whole process out of line. We used a small piece of wire twisted around the string to mark the center of each pole. We used left over blasting cap wires, but i think today's telephone wire would work just as well. Since 6 x 6's vary in dimension quite a bit, always work to the center of the pole, rather than relying on an edge (except at the corners, obviously). Plumb your poles both directions as you backfill and/or mud in. Throw some braces on them until you get the girts nailed on. If the poles have some twist to them, use the braces to lean them in or out as you girt and sheet the building. Good luck. I am tackling a 12' x 30' addition to an existing pole barn right now, too.