Ctrl+S will save the file. That keyboard shortcut works on almost all Windows programs, including VS Code, Atom, MS Word, Excel, etc.
You can make the normal “file” menu visible in Atom in the settings. I’ve attached a screenshot. PlatformIO is just a command line tool and an extension for an editor. The editing program is either VS Code or Atom and basic functions like saving are part of the editor and not of PlatformIO. Have you decided to stick with Atom? I’m only asking so I can give you screenshots of the right editor.