I have 2 bush bean plants, should I prune these to a single stem if I'm growing them in a square foot garden? I'm not familiar with growing beans, so caring for them is all new to me. This is the variety: http://www.seedsavers.org/pencil-pod-golden-wax-bean
Allow the side shoots to grow.
Bush beans are bred to be bushy, so by removing them you're fighting the plants' natural growth habit. The side shoots also carry leaves, which will provide more energy for making baby beans, and flowers, which will turn into those baby beans.
The typical spacing that I've seen for bush beans is 6" between plants in a row, so you should have more than enough room in a square foot for one plant.
Note that the variety you have, Pencil Pod Golden Wax beans, are a bush bean, but the page you linked to actually contains instructions for pole beans, which have different support requirements:
Pole beans are usually planted closer together than bush beans, and grow as vines so they require support such as wire or string netting or a trellis to grow on.
Bush beans are free-standing plants that don't generally need support unless they happen to grow very tall or have a heavy crop to pull them over.