J401 flashing - add configured pinmux dts files

Hi,
I followed guide mentioned here Flash Jetpack | Seeed Studio Wiki
In this guide I flash NVIDIA L4T 35.3.1 to install Jetpack 5.1.1 on the reComputer, exactly as mentioned in drive.
However I want to change 40 header pin configuration. I created new configuration from pinmux sheet but I do not know how to link it to this installation.