You open Civ3MultiTool, you open the SaveGame Modifier and then you load a savegame, maybe "/Civilization III/Conquests/Saves/test.SAV".
You go into the Map tab, choose export and a file to export it into, maybe "/Civilization III/Conquests/Scenarios/test.biq".
You open the standard scenario editor of C3C. You open the before mentioned biq, alter the terrain and save it in the same file.
You switch back to the still open SaveGame Modefier and import the biq file, maybe "/Civilization III/Conquests/Scenarios/test.biq". Then you save your savegame.
Please note that i did not try this procedure. Also note that certain terrain changes may create problems. Cities are not meant to be on sea tiles etc.. Also there might be other issues that i even failed to image, yet.