Not completely sure i understand your question but hopefully this will help.
Step 3: west flash
This builds your application then flash your device.
So steps to flash your application are:
Step 1: Identify port
Find port on Linux
This is defined at 'scripts/west_commands/runners/bossac.py' as
DEFAULT_BOSSAC_PORT = '/dev/ttyACM0'.
Update the port identified in Step 1
Step 3: Build and Flash Board
Run West Flash
If configured correctly West will build and write application to board.