The layered filesystem Aufs is great, it underpins the architecture of Puppy linux, for frugal installs, etc. Aufs superceded the much older and now defunct Unionfs.
Aufs is available as a patch for the Linux kernel, however something else called Overlay fs made it into the official kernel source. Overlay is not as capable as Aufs.
Currently with "QuickyPi", I am using the standard pre-compiled kernel (right now, using 4.4.19), which does not have Aufs, only Overlay.
Note, the kernels compiled for puppies, at least as far as I know, do not have Overlay enabled, so you can't use it, only Aufs -- ditto for Quirky prior to now.
I want to change over to using Overlay in Quirky. The first step, is I want to run woofQ from a Pi2 or Pi3, with only Overlay available. The scripts '2createpackages' and '3builddistro' make use of Aufs during build of the distro, so I have modified those scripts to use Overlay, if the kernel supports it.
Later on, I will have to look at frugal install of Quirky, which currently uses Aufs.
Note, the reason that I am running woofQ in the Pi, is to do a native build of the Quirky distro. This has certain advantages, such as being able to chroot into sandbox3/rootfs-complete (which 3builddistro does in a few places) -- otherwise, 3builddistro does a "cross build", which delays certain operations until the Quirky distro is booted on a Pi -- resulting in a very slow first bootup.