Install the mod you downloaded, most of the time you simply copy and paste the files into your FO2 directory, some people get confused with the directory structure i.e.
Check your FO2 folder, for a file called patch000.dat, if you have it delete or rename it.
Install the version of Fallout 2 that takes up the largest amount of space i.e.
Generally mods contain a "readme" file with a guide, I would recommend checking that out, before proceeding with this general guide, also before you attempt to install a mod, make sure FO2 works fine vanilla: