How to Upload Server Files to VPS?

I have a VPS, but I don't know where to upload files.
Do I just upload Trapped's Realm Files through FileZila onto my server? How do I set up MYSQL?
Do I use Linux? (Debian, CentOS, or what?)

Please help. I will give you Full Admin if you help me succesfully.

---------- Post added at 04:47 PM ---------- Previous post was at 04:41 PM ----------

Also Trapped's Files, Vault files seem broken and I don't know how to make guilds work.

you need to do several things if you just downloaded the source from trapped's git.

First you need visual studio to compile it to run.
second i'll advice you to run windows on your vps. unless you know what your doing and will use mono and run it on linux.
third install software like, .net 3.5 and 4.0 and mysql server
fourth you import the struct.sql into the mysql server in the database "rotmg"

From there on there are several guide to do from there..