SW doesn"t handle any Zinnser products, but Ben Moore does. My local HD doesn't carry it and won't order it, but yet they carry Zinnser, figure that out. I ended up finding it at just a small paint store in the area.
You are giving conflicting info here. As Brushjockey mentioned Primers are not for covering colors. Any patched areas will need 3 coats or they will not match the existing wall. It is always best to have your first coat be primer and then a coat of paint (both of those can be on just the areas patched), and then a final coat over the entire wall. One coat of primer and one coat of paint is rarely enough, especially with an eggshell or semi-gloss paint.
I can see how it comes across conflicting... When you say three coats, do you mean spot prime and then two full coats on the entire wall or just the spot primed area?