For the queries about the basics of stress tensor, it is better to find out the answer in textbook by yourself. Otherwise, a simple answer here cannot help you to capture the whole background of stress tensor, strain, pressure, and elastic constant and so on.
1. The pressure is usually taken as the average of sigma_ii (i=1,2, 3, i.e., xx, yy, zz), i.e., the diagonal terms.
2. You can do a simple test calculation: calculate the stress tensor for a cubic structure at two different volumes (one is much smaller the equilibrium volume, and the other is much larger than the equilibrium volume). From the reported values including sign at these two different volume, you can get the "sign rule" for the definition of stress tensor used in the ATK.
3. At the equilibrium state of a given pressure, the non-diagonal terms are usually close to zero (i.e., very small value) and they can be neglected.