Local overlays should be managed via /etc/portage/repos.conf/.
To enable this overlay make sure you are using a recent Portage version (at least 2.2.14), and crate an /etc/portage/repos.conf/brother-overlay.conf file containing precisely:
[brother-overlay]
location = /usr/local/portage/brother-overlay
sync-type = git
sync-uri = https://github.com/stefan-langenmaier/brother-overlay.git
priority=9999
Afterwards, simply run emerge --sync, and Portage should seamlessly make all our ebuilds available.
Add https://raw.github.com/stefan-langenmaier/brother-overlay/master/repositories.xml to overlays section in /etc/layman/layman.cfg.
Or read the instructions on the Gentoo Wiki, then invoke the following:
layman -f -a brother-overlay
After performing those steps, the following should work (or any other package from this overlay):
sudo emerge -av media-gfx/brother-scan3-bin