Although the excavation itself demands only fairly rough measurements, when it comes to lining out the footings, you'll have to muster all the accuracy you can. A Container House builder's level (wielded by someone who knows how to use it) will provide the best results, but you can get by with some wood scraps, mason's twine, a carpenter's spirit level, and a 100-foot measuring tape.
I'd suggest that you use the process of triangulation to ensure that your foundation layout is square. As you likely know, Pythagoras, the Greek philosopher, discovered that the square of the long side of a triangle is—if the other two sides are perpendicular —equal to the sum of the squares of those other two sides. In building, we usually work with what is known as the "3-4-5 triangle," simply because it's so easy to measure.
To line out a foundation using 3-4-5 triangulation, first set a stake with a nail in its top at one corner of your proposed structure. From that stake, measure two sides of the house, eyeball a perpendicular corner, lightly set stakes at the two new junctions, and stretch twine between the three posts. Now, check the squareness of the right angle by marking the intersecting lines at points three feet down one string and four feet down the other. The shortest distance between these two marks should be exactly five feet. (You could work with a 6-8-10 triangle, or any other multiple of 3-4-5, and doing so would provide even greater accuracy.) Continue by staking the fourth corner and rechecking the triangulation (the process is time-consuming, but don't rush it!). Once you're satisfied with the layout's squareness, level the stakes by checking the string with the carpenter's level and adjusting the corner heights as needed.
Batter boards are simply frameworks, set beyond the foundation area, from which lines can be stretched to indicate either trench sides or centers. When you stretch the strings, compare them with your stake tops to see that they're level and in line, and then double-check the measurements before you start digging.
If your excavation was fairly level to start with, you may be able to cut the trench for the footings right into the exposed subsoil. Trenches should be cut with smooth vertical sides, and you should check for the correct depth from the lines. The bottom is normally 16 inches below floor level, but it may be deeper under door thresholds or where there is no berming (the bottom of the footing must be below the frost line). When digging, you'll have to remove the original stakes, so the lines stretched between the batter boards will end up marking the building's boundaries.
If, however, trenching isn't appropriate for your soil type, you'll have to form footings on the excavation floor with braced and anchored 2 × 8's. (Once the concrete has set, the boards will be removed.) In this case, your Granny House level will be 16 inches above the excavation bottom, and your base course (we'll get into that in a few more paragraphs) will be 12" deep.