Publish vs Deploy

Question

Hey Guys

I want to know what is the difference between publishing your app or creating a setup file??
In the setup file I can add EULA, which is cool, install it in C:/Program Files, or wherever you want to intsall it, but then I can't write to the text files, e.g. I use a text file to store customer information, but gets an error when want to do so, but if publish my app, it works perfectly.