Keys and LED outside matrix

Hi there! I have build my first keeb and now i play with firmware a little. I use cheap clone of rpi pico and I’m happy with this controller:)
Now I realize that I have 2 more buttons from encoders and 1 more on controller (usr button)
Additionaly I have 1 more WS2812 LED on controller. So i have reasonable question: is it even possible to handle clicks for encoders button and use WS2812 for example to indicate layers of my keymap in different colours?
I understand that for QMK you must set up all buttons in one matrix and also LED must be part of chain
But what if I have encoders buttons (and of course onboard usr button) outside the matrix? what if i have one more RGB LED? Is it my personal fail in design or i can utilize all avalilable things?

I appreciate any help and info!

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