To find out which version you possess ...
Open a game, press Game | Game Options from the menu - you get a pop-up menu ...
The title bar of that menu contains the game version.
It should say:
- Civilization II 2.42 Custom 08-Oct-96 if you are playing basic Single Player Civ
- Civilization II 2.7.8l Scenario Editor 21-Oct-97 for Fantastic Worlds - or
- Civilization II Multiplayer Gold 5.4.0f Multiplayer 26-March-99 Patch 3 for the Multi-Player variant
If your game is 'straight out of the box' it is unlikely to say any of these, but should resemble one of them closely enough for you to know which patch you need to come up to speed. If you have any doubt, please post your version info and I'm sure one of us will be able to point you in the right direction.
As for the 'Main Civ Directory' for SP the game only looks in the directory in which the game is loaded (IIRC by default that is C:\mps\civ2\ ) both FW & MGE are more intelligent and pick up scenario files and save games from a designated directory.
It is essential that scenarios be played with the version of the game for which they were designed (although it is possible for SP scenarios to be played in FW & MGE & FW scenarios to be played in MGE - things tend to go wrong such as America declaring war on the UK in a WW2 scenario)
Hope this helps ...
Good civin'