Okay, so just as a starting off point, unless you have MB set to automatically scan for files at startup, you have to manually do it in some fashion or another. You can do this in one of two ways;
1. Click on the Musicbee menu dropdown, File, Scan Folders for New Files.
2. Use the Hotkey, assignable in the preferences (ctrl+o). I don't remember what it is by default, but I made mine "Insert" for simplicity. I'm inserting new files, so it makes sense.
Another useful hotkey to remember is a rescan for when/if you're updating metadata tags and it doesn't automatically refresh, or if you've changed it outside the program. Again, it's assignable in preferences (ctrl+o) under Hotkeys, File: Rescan Monitored Folders (Will do your entire library) and File: Rescan Selected Files. These options are just above the one for File: Scan folders for new files.
It doesn't appear that the rescan really shows up anywhere else though, so it might be hotkey only.