They do not have to be used together. To explain further lets say you have created a VI to be used as a subvi in a main app. You may want that subvi to be called when you press a button and this vi will always open its front panel. In this instance you would use method two. Now lets say that you created a subvi that can be used in many different main applications then you would set the window appearance as want it but do not select the option of open when called. Then you can set whether or not the front panel is shown using method 1. I hope this answers your question.
Joe
