First off, don't worry too much about screwing the game up too much. You can always reinstall and apply the patches and you'll be right back where you started. So you can always fix any damage you have done. Provided you have the CD and the patches available.
Second, always make bakups of any files you're going to change, so you don't have to reinstall.
Third, start small. Don't go in and change every little thing you feel like changing! If you do something wrong, it will be very hard to find out what it is you added that is making the game crash, since the game provides no helpful error codes to tell you what's going wrong.
So, in essence start by adding one unit for example. Get that down and working. Then maybe add a couple more. Add one tech, get that working, then add a few more. Adding techs and civs are some of the trickier aspects. Adding buildings and units is pretty easy. Wonders and small wonders require a few more steps (wonder splash screens must be set for them)
Look up information on that one particular thing you want to do in the forums so you know what to do/not do. Otherwise you run the chance of being overwhelmed by how many things it is you have to change at once.
Finally, keep multiple copies of your mods. That way you can always revert to a previous stage in case something goes wrong.
About the editor looking different from the game, it's probably because the editor is at a different magnification than the game. At least in my computer it is. I think it all depends on what resolution you play the game in and at what resolution your desktop is. Other than that, I wouldn't know why you're seeing this difference. The editor takes the terrain information from the Civ3 art/terrain files and changing those will affect both the editor and the game equally. So I don't see how you could be seeing significant differences.
Anyways, most of it is just common sense, I'm sure you probably knew all this. Just go ahead,and start modding, it's about the only way you'll learn effectively.
