The Instructions to install mods vary slightly from one to the other so you will have to be more specific about which one it is you're trying to install.
There are a lot of choices out there as far as stalker mods go. One good one could be 'Priboi story', it's a completely new storyline. I'm not certain, but I seem to remember that it's a standalone mod so it would be easier to get up and running.
A good place to look would be: Mods - S.T.A.L.K.E.R. Shadow of Chernobyl Game - Mod DB Most of the mods there come with pretty solid directions to install(Either on the download page or in a text file contained within the downloaded files) If not, then there's a big community of people there that will more than likely help you out.
Also if you havn't already, buy a good cheap copy of the other Stalker titles('Clear skies' and 'call of pripyat') both are good and in the spirit of the original.
I hope this helps.