MyBB Community Forums

Sometimes, when I upload a plugin's contents to my server, many items in the plugin already exist.

Well? What am I supposed to do? Overwrite or skip? If I overwrite, maybe I am deleting something important that was updated recently, no? And if I skip, I risk myself rendering useless my plugin, right?

What files are already there? If you are overwriting plugin files, it's likely that you are updating it. The only MyBB core file that is often changed is ./inc/functions.php

Just make a backup of your forum now. Then upload the plugin. If it breaks the forum, just reupload the backup