It should detect the keyboard and set it to bootloader mode automatically, prior to flashing firmware.
I've found that I need to remove the previous build/file before making a new one as it doesn't overwrite it; but this might just be my personal experience.
-See [build environment setup](https://docs.qmk.fm/build_environment_setup.html) then the [make instructions](https://docs.qmk.fm/make_instructions.html) for more information.
+See [build environment setup](https://docs.qmk.fm/#/getting_started_build_tools) then the [make instructions](https://docs.qmk.fm/#/getting_started_make_guide) for more information.
Note that this is a complete replacement for the firmware, so you won't be
using Bootmapper Client to change any keyboard settings, since not all the
projects / qmk_firmware.git / blobdiff