When you save a file in a blank Atom window, the directory that file is in is automatically added as a project folder. When you save additional files, Atom will assume that they’re going to the same place. For how Atom thinks about projects, this is very reasonable (and since Atom is Atom, its behavior will differ from Word/Libre/Notepad which don’t have any opinions about projects). To circumvent this, just add a new project folder for each additional place you intend to save files for a given Atom window. Once you have a project folder added for a particular directory, you can simply right-click on anywhere in the tree view and select
New File to create a file in that specific folder and not have to deal with the
Save As dialog at all.