I’m not sure what function you’re using to flash the board, but if you use the Run (Ctrl-F11) command from the Run menu, it will flash your latest build of the firmware onto your target, then reset and run it. I think this is the function you’re looking for.
I don’t recall if Run -> Run requires a pre-existing “Run configuration” to be created or not. You may be prompted to set one up the first time you attempt to run your application this way. You should be able to use default settings with the “AC6 STM32 Debugging” template if you are prompted to create one.