If you use the installer and tell it to 'get you the works' it should download and place most it where is needs to be, but if you want to do it by hand then:
Core files should go in: Freespace2\fsport\
Port MVPS: Freespace2\fsport-mediavps\
Awakenings: Freespace2\Awakenings\
Cardinal Spear: Freespace2\Cardinal Spear\
Basicly most mods go in their own folder, and some mods call upon other mods which require the folders name to be a certain thing. An example of this would be Cardinal Spear calls upon FSPort and FSport-mediavps so the folders must be named that. For almost all mods, the thread you find them in will tell you how to install it, what goes where, and what things must be named. When in doubt, use the installer.
3.6.12 MediaVPS (FS2)
http://www.hard-light.net/forums/index.php?topic=70736.0 goes in Freespace2\mediavps_3612