The very first thing you need to do is to run the unpacking program CA have published. I think it's included in the 1.2 patch or on the Kingdoms disk. It sounds to me like either you haven't done this yet or it hasn't worked properly. If it's worked then your "data" folder should contain two files with "geography" in the name, plus a whole bunch of other files and directories. These two geography files are the ones you need to delete, but if they aren't there to start with then the files haven't been unpacked.

You could try reading the readme that comes with the unpacker if your having trouble with the tutorial.

Most of the files are originally marked as "read only" which is probably why you can't save them. You need to uncheck the box for this in the properties dialogue.

You then need to set up a batch file to run the game from your modded files rather than the packed files, otherwise none of your changes will appear in the game. Alpaca and the readme both explain how to do this.

You don't need any other programs besides the unpacker itself and notepad to get the game set up for modding.