I don’t have an SKR v1.3, but I took a look at some pinout diagrams. I looks like you have two choices:
Assuming you are powering your board with 12V, the “Case fan” pins should provide 12V any time you have power to the board.
You should be able to control the 4020 fan pins through g-code. See M106/M107. You can get your CAM software to automatically output the M106 and M107 commands so the fans would only be running when your job is running. This is how I control my spindle (using fan pins).
You can just wire them straight into the 12V coming into the skr. Then they will be on whenever the skr has power.
There are firmware options for a case fan, or a motor cooling fan, which are both good options. But not worth setting up to compile the firmware yourself (IMO). If you want to try it out, start with the firmware from the zip you linked and build that first. Then make one change at a time while compiling the intermediate changes.