You're not done setting up your shader yet. By looking at the layered texture attributes, you have the dirt texture blend mode set to "over" but you have no masking texture (the patchy texture you painted) plugged into the "Alpha" channel. This is what controls the transparency of the associated layer, and right now it's in a 100% uniform opaque state.

To your second question. Maya does not save the state of the Hypershade work area whenever you close the window, as Pixal said, you'll have to graph the connections or drag the nodes in.