The goal, of course, is to get as much performance as possible, which means using the lower angle (30 degrees). But, you have to balance that off against robustness: depending on the knife and how you're using it, you might have to back off to the 40 degree angle if the blade starts chipping or rolling too much.
My general rule is: For folders, you should be sharpening mostly at 30 degrees. Sharpen the entire knife at 30 degrees -- raise a burr, grind it off, finish it at 30 degrees. Then, put it on the 40 degree stones and take a couple of light (no more than the weight of the knife itself) strokes per side, to refine the final edge and remove the remnants of the burr.
Again, for a folder, this edge will give you great performance, and hold up just fine. [Note that Esav seems to be a little more conservative than me on this]. This is the highest performance edge possible on the Sharpmaker, and I do not back off this unless I see that the particular knife I'm using is getting its edge damaged ... in which case, I'm tempted to suggest you just get a better knife
If I do want a thicker edge, a next step might be to go with the 30 degree angles, and using magic marker on the edge, take the edge down until all the magic marker disappears, but before a burr gets raised. Then put it on the 40 degree hone to raise a burr and finish up.