eselect-repository is essentially a wrapper to edit
/etc/portage/repos.conf while (optionally) using the database of known overlays. Once that's done, any of emerge --sync / eix-sync / emaint etc... will start sync'ing those overlays alongside ::gentoo without further actions.
Alternatively, you can edit repos.conf yourself and control everything. The two above links should have most answers.
Edit: adding a local overlay to repos.conf is just 3 lines of config, see [localrepo] example. You can probably add it with eselect-repos too but I never tried
