When using L metal or angle iron, if one flange is vertical and the other horizontal, and if the horizontal flange is on top and under compression because it is bearing a load across a span, does one use the maximum or minimum section modulus for completing stress and deflection calculations?
Well for a given beam shape the moment of inertia I is constant. Your loading scenario, which you know, determines the distance y from the neutral axis to the extreme fiber. So, section modulus I/y is also constant. Find the centroid of the shape, its position vertically, and take the larger of the two numbers -- that's y.
To try to answer your question more directly, first I'm going to assume you're dealing with angle iron with unequal leg lengths. Then I'm going to assume that by "minimum" and "maximum" you mean that you found two formulas in a table; one for the section modulus w.r.t. the neutral axis when the short leg is vertical in the scenario you described (answer to your Q: "minimum"), and one for when the long leg is vertical (answer to your Q: "maximum").
Only the sign of the elastic flexure formula cares whether the top or bottom is in compression -- your convention tells you that (positive bending moment in the case you described). You only care about that if you're dealing with a material with unequal strengths in compression and tension (e.g. concrete), or if your expected failure mode is buckling.