Hello Jay Hunt,
I would like to confirm that you are using the FSL Community BSP.
The Device Tree sources you would need to change would be those of the first location
/opt/yocto/imx-yocto-bsp/build/tmp/work/cortexa7t2hf-neon-poky-linux-gnueabi/linux-libc-headers/5.4-r0/linux-5.4/arch/arm/boot/dts/imx6ul-14x14-evk.dts
The u-boot device tree is independent. However, usually you won’t need to change the u-boot device tree unless some of the new hardware configuration would need to be reached from the bootloader.
Also, keep in mind that Yocto is not meant for development but rather distribution, so it won’t keep track of changes on the source code. You may want to try to run a bitbake clean and then bake again, but there is not guarantee that the changes you made won’t be discarded. It is recommended to cross compile from the source code to test your changes and then make an append to change the original recipe in Yocto.
I hope this helps!
Regards,