We have a feature request for that https://github.com/platformio/platformio-atom-ide-debugger/issues/1
Nevertheless, PIO Unified Debugger is universal, it isn't linked with PIO IDE for Atom and could be integrated with other IDEs, including Eclipse, VSCode, or even VIM/Emacs, etc. We will update our docs later and explain how to do that.
Also, with PIO IDE for Atom, you can debug simultaneously more than 1 target. It could be achieved via different
platformio.ini. Here is the question: from the which instance need to remember the last breakpoints?