The qLinux overlay is intended to overlay ebuilds of the (default) Gentoo portage tree.
The qrtools overlay introduces some new categories:
qrt-apps | ebuilds which are not in the gentoo portage repository | ||
qrt-base | tools und utilities of the qrtools project | ||
qrt-virt | wrapper ebuilds which replace a program by a (usual better) one, they do nothing install by itself (like virtuals)          |
These are overlayed packages:
There are different techniques:
Here we have an ebuild in the same category and with the same name in ::qrtools like in ::gentoo. The ::gentoo ebuild will be mask in  package.mask/qrtools 
:
sys-process/cronbase::gentoo
The typical use case is to eliminate ::gentoo packages which are a dependency for others.
Here a ebuild of ::gentoo will be patched. Thus some functionality of the ebuild will be changed. An example is sys-apps/baselayout-2.4.1-r2 where the faulty check of the symlink  /usr/local/lib 
will be removed. Anyway, as this is a risky change it will be not used if other possibilities exists.
Patching an ebuild is configurable through  /etc/portage/qrtools.conf/postsync.conf 
:
P:sys-apps/baselayout::gentoo
The leading P defines that this ebuild will be patched. (see internals for details)