If you are using Windows, your saves are stored in
AppData -> LocalLow -> Anduo Games -> ThirdCrisis -> saves
Outside of the game folder. So "if your saves are compatible" you should simply be able to load them from within the game after installing the new version without having to do anything. If you want to know for sure, don't delete the older version of the game until you know that your save file will work for the new version first. Install the new version of the game in a separate folder to test.
Also see: Guide to Save Files Vilsa from Anduo Games has so kindly posted above.
Note: I've known games to break or get very buggy by loading save files from older game versions with other games.
Not sure about this game though. Play with old game save versions & use them at your own risk. You've been warned. Let everyone know how it works out. Mine seem to work thus far, I'm sure there is no reason to worry...