VIA Configurator uses the "dynamic keymaps" feature I added to QMK, which will let you change keymaps without needing to compile QMK. It works by storing the keymaps in EEPROM memory, i.e. memory that will persist after a power cycle, and can be changed at runtime of the firmware. The backlight settings are also stored in this memory.
VIA Configurator works by communicating over USB with the keyboard firmware, and doesn't require uploading (flashing) new firmware to change keymaps etc.
Holding Esc when plugging in USB will invalidate the stored settings in EEPROM, and also start DFU bootloader so you can upload new firmware if you want. Invalidating the stored settings in EEPROM is useful if you want to install new firmware, but a side effect is that it can restore your PCB to "factory defaults". This is because the next time the firmware runs (whether the same firmware, or new firmware), it will load new settings from the firmware into EEPROM memory.
If you want to build your own QMK firmware (because you're a power user and want full control), you will probably want to turn off dynamic keymaps by adding DYNAMIC_KEYMAP_ENABLE = no in the file rules.mk in your keymap folder, i.e. /qmk_firmware/keyboards/rama/m60_a/keymaps/blahblah This will turn off dynamic keymaps so that it will only use the keymaps you define in keymap.c and never use keymaps in EEPROM. This will mean you can't change keymaps with VIA Configurator.
If you build your own QMK firmware and don't turn off dynamic keymaps, then install new firmware, if you didn't do the Esc/power on trick, then changes to keymaps in the firmware won't get used - it will still use the keymaps that were stored in EEPROM (i.e. from a previous firmware and/or changes using VIA Configurator). If you do the Esc/power on trick, then the keymaps in EEPROM will be reset to the keymaps in the firmware.
Note that the above also applies to backlight settings, if you're changing things like colors in code, they are only the defaults that get loaded into EEPROM memory.
You can use VIA Configurator for changing backlight settings while using a custom-built QMK firmware, as long as the firmware still has the code required for communicating with the host, and hasn't drastically changed things like keycodes.
What VIA Configurator can't do (yet) is know about any user-defined keycodes you may have added to your custom built QMK firmware. It also cannot handle changes the existing keycode values, i.e. if you change the order of keycodes in QMK core code, or turn on features that change this order. We're working on making it more tolerant of these things.
TL;DR VIA Configurator and "stock" M60-A firmware caters for most user's needs, by providing you with a simple way to change up to 4 layers of keymaps and change the backlight settings, without needing to build QMK yourself and do a slow and sometimes problematic upload of new firmware.
