Every X window is a buffer, so you have all of emacs's powerful buffer switching programs (see: ido, helm [1], ivy [2]) for focusing windows. Also there are multiple interesting solutions to managing window splits [6], moving windows [3][4], saving their configuration [5], etc.
[1]: https://github.com/emacs-helm/helm
[2]: https://github.com/abo-abo/swiper
[3]: https://www.emacswiki.org/emacs/WindMove
[4]: https://github.com/abo-abo/ace-window
[5]: https://github.com/Bad-ptr/persp-mode.el
[6]: winner-mode, one of my favorite things. https://www.emacswiki.org/emacs/WinnerMode