Ayia, I'm sure he's confused as hell now.
As far as I remember, the Bonus Pack installer needs to know the root directory of your X3R installation. That would be C:\Program Files\Steam\steamapps\common\x3 - reunion
If you're installing a script that comes in an SPK file, it requires
Cycrow's Plugin Manager. I believe this version is compatible with Reunion and Terran Conflict scripts. This is a totally separate program, and so can be installed anywhere you wish.
If you are manually installing a script, it goes in C:\Program Files\Steam\steamapps\common\x3 - reunion\scripts unless it has accompanying language files, which go in C:\Program Files\Steam\steamapps\common\x3 - reunion\t
There should be directions in the thread belonging to the sacript, in the Tutorials sticky, or packed inside the script RAR/ZIP file in the form of a readme.
If you want to install a single mod file, it goes in C:\Program Files\Steam\steamapps\common\x3 - reunion\mods and will have to be selected at the splash screen when you start the game. You can tell mods apart because they come in the form of a pair of files called a .cat/.dat pair.
If you want to install multiple mods, you'll need to do A LOT of reading about "fake patches" and "merging" mods.
Scripts and mods bring many, many wonderful and awesome features to the game, but it has its own learning curve. Expect to have to reinstall the game (thereby possibly losing your savegames unless you keep strict track of everything you install[HINT HINT!

]) quite often as you get the hang of things. Once you begin to understand how the game engine itself works, implementing these things will become much easier for you. I recommend reading through some of the guides in the Tutorials sticky to get acquainted with what you're dealing with.
Welcome to the Universe.
