MCU Firmware

Its likely if you are migrating from Marlin (for instance for a Ender 3 V3 SE), you will need to flash new klipper firmware to the mainboard (this is not the same as the RPI), and for the moment at least this guide is lacking a lot of details for that.

I think the easiest approach here is to install Simple AF and acccept that the MCU likely won't connect and then login to your RPI and use make menuconfig and make to create the firmware so you can get that flashed in whatever method is required for your mainboard.

Creality mainboards in general require the use of an SD-Card to get this done, BTT boards can sometimes be flashed from the cli on the printer (ymmv). Please consult manufacturer instructions where appropriate.

Ender 3 V3 SE

The Ender 3 V3 SE is a bit painful to flash, and it depends on which version of the board you have (C13 vs C14), but there are a few guides this one looks to be the most detailed:

For building the firmware: https://athemis.me/projects/klipper_guide/#create-printer-firmware-bin-file For getting it onto your printer: https://athemis.me/projects/klipper_guide/#flash-3d-printer

SKR Mini E3 V2

Its important to ensure the !PA14 GPIO setting is configured, but even more important for RP3 is to ensure that the config.txt setting dtoverlay=dwc2 is enabled in the [all] section, otherwise klipper is going to crash the entire pi every time it tries to start up and you will racing to stop it after ssh into the pi to deal with this after the installation.