Manual changes can be done in the subfolder "<plnx-proj-root>/project-spec/meta-user/"

U-Boot	recipes-bsp/u-boot/files/platform-top.h	overwrite, add UBoot settings
Device Tree	recipes-bsp/device-tree/files/system-user.dtsi recipes-bsp/device-tree/files/pl-custom.dtsi	overwrite, add device tree attributes
Kernel	recipes-kernel/linux/linux-xlnx/	changes with "petalinux-config -c kernel" will be add here automatically
Apps	project-spec/meta-user/recipes-apps	add simple new app with "petalinux-create -t apps -n myapp --enable" enable/disable with "petalinux-config -c rootfs"

PetaLinux 2018.3

PetaLinux Installation

...