Maybe in next versions and updates (not soon) i will add raw git repository with hidden .git folder and portable git client, who knows. But for now i don't have a time for that. Just start with what you have, be sure, after some research how is configured, you will understand what setting is for, and when you decide to make your own server, you can always use rAthena folder from the pack as real example and compare with rathena taken from github repository to avoid mistakes or errors. About client side, it's not so easy at all, because client-side managed by 1 guy, and better if author of client-side will answer buy himself.
about "how make your own server-side" which you will be able to update.
First of all watch the video, to understand theory.
then, download any normal git client, like: SmartGit, or SourceTree, or GitKraken
then, with Git GUI Client clone official repo from github to your PC: https://github.com/rathena/rathena/
then, take Visual Studio Community Edition 2015 (yes, size of it 8GB (LOL)) and install it (C++ support must be added in installer) you will use it everytime when sources changed to recompile your server.
then time to time just watch on rathena github repo, and if new updates comes, just grab them via "Pull" (see video above, and you will understand)
configuration part how to setup rAthena you can read here at forum. And see examples of configs at configured by me rAthena folder in the pack.
Rest guides how setting Up rAthena - you can find in official wiki or here at forum (use search) https://github.com/rathena/rathena/wiki
OpenServer from the pack you will use as your MySQL server, because it's most powerful and most easiest solution what you can find at the market, which not bugged, and not complicated, and at the same time clean, stable, and effective with nice gui and set of tools which of course (at least phpmyadmin) you will use in your real life when you will learn rAthena.
But the best what you can start to do, it's start to read complete documentation (yes, it's not good, and i hate it a lot, but i have bad english, and i can't suggest better documentation which available now at rA).