Go to the menu bar at the top of Atom. You should have a Juno tab with a lot of options. Scroll down to settings and the Julia Client settings pane will open. There you will find a Julia executable path. Fill it with the julia.exe like: C:\Julia-1.3.1\bin\julia.exe.
You can also check: Juno - JuliaLang. The developers post periodically stuff about updates.