Question about VPS and WordPress

Hey there WordPress community,

I´ve got a question about making WordPress work on a VPS.
I don´t know if this is the right place to ask but hell.

I´ve got a VPS set up with Installatron, which handles basic WordPress installations. Now when I add a new user through DirectAdmin (reseller) and run a WordPress installation all is well, I can upload files through the media manager (images, plugins and such).
However when I go and overwrite files (such as the whole of WP-content when I’m moving a website) the User/Group gets all botched.
I can either upload through FTP (chown -Rv user:user path) or upload through WordPress (chown -Rv apache:apache path).

Is there a way to set this up properly? I’m quite new to command lines and Linux and only recently started doing things like this. So be easy on me! 🙁

Thanks in advance!