There are actually some "modpack managers". Small programs that swap around files for you so you can choose which modpack to play. I've never used any of them so I don't know exactly how they work or where you can find them.
A slightly less elegant solution is to do the following:
- put your modpacks in separate subfolders of Civ2 (like you would put a scenario in its own folder)
- start a regular game
- save your game at the very start, into the modpack folder.
- reload the game from the modpack folder... and suddenly the modpack rules and graphics are loaded.
This might not be feasible for all modpacks, though. If, say, the modpack changed the starting unit so it's not a settler-type, then you and especially the AIs could have built cities in the first turn before the modpack rules were loaded... And, for example, with that Middle-earth modpack, you'd have to start as, say, the Romans before loading the modpack, and then only after reloading would you become the equivalent Middle-earth civ.