I just wanted to chime in because I think YellowEagle was vague and may have made a mistake that if followed could cause problems for people.
In the Stalker game folder you want to edit the file called "fsgame.ltx" with a text editor. The following is the line you want to change to "true", already changed in this example.
$game_data$ = true| true| $fs_root$| gamedata\
Also as you can see it refers to "gamedata". That is the name of the folder that will be used for mods, whatever it's named in this file is the name of the folder that will be used by the game.
Basically files put into that folder will override default game files but the game will not look for them until this is set to "true".