Installing an Arma3 PBO is a process that when guided is something that is easily repeatable and something that adds much more playability to the standard arma3 game.
Begin by locating your arma 3 installs multiplayer scenario folder, this graphic illustrates where that folder is located.
Simply upload scenario pbo files to that folder, now you'll want to configure your server to play the scenarios you added.
You'll need to go into your configuration files on your manager.gameserverkings.com panel and edit the configuration for A3Master/CONFIG_server.cfg
Find something that looks like this:
// MISSIONS CYCLE
template = "explorealtis.altis"; // Filename of pbo in MPMissions folder
difficulty = "Regular"; // "Recruit", "Regular", "Veteran", "Custom"
Edit the explorealtis.altis to the name of your pbo file without the .pbo extension and reboot our server, you'll now be using that scenario!