Question about overlaying certain stage

[BetelGeuseee]

What I am doing:

I created a custom stage3 directory where i included a binary executable that should be copied somewhere in the rootfs. I modified the 01-run.sh script. Also i need some directories to be created while building stage3, but in the final image these changes are not reflected.

Is there any standard way that i should know or follow for overlaying my custom stage?

[XECDesign]

Do you have an example of what you've done and what's not working?