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!