Your changes will not affect existing games. Firaxis has removed this possibility for more than a year now
I don't remember having ever seen a scarcity setting for resources. AFAIK, 2 resources per Civ will be spawned in a random map game. However, I never put much interest in this part of the editor, so maybe someone will correct me.
To preserve random seed (or not), you don't need the editor. In the game, you have to check/uncheck the box when beginning a game. This box appears in the "Pick Civilization" screen, next to the victories you want, culturally-linked starting positions, etc.
You may save your own rules in two ways:
- either you change the default rules and always play with your own. In this case, you should change the "civ3mod.bic" file. You should save the original file in a safe place before however, to restore it if something goes wrong with your own rules.
- either you create a set of modified rules that you'll use from time to time. You should then save your modded rules under any name (.bic). You'll then load this file with the "load scenario" button at the beginning of a game.