Make a backup copy of your SMAC/X game folder
Copy the contents of the mod folder into your SMAC/X game folder.
Click 'Replace all'
If you are playing SMACX copy from folder 01 and it will replace the Crossfire factions.
If you are playing original SMAC then copy from folder 02 and it will replace the original factions.
(If it all goes horribly wrong and you've lost your unmoded copy of SMAC, you can copy the contents of the folder - Restore Original SMACX- into a copy of the moded game folder and recreate the original game.)
Remember not to mix and match factions when setting up a SMACX game, because the CA5 factions are on a different power scale to other factions. :)