Like if I take the clear weather area copy the ini and paste it but add different variables will that add to the options of clear weather or will it break the game?.

You can pretty much do whatever you want with the Weather variables. I can't imagine it would break anything.

Just be sure to make a back-up of your ini, because it's easy to get unwanted effects when you start modifying things.

What do you mean by this? You can't add new tweakables to weather. For instance, you cannot make clear weather have particles (such as snow or ash) or make clear weather have thunder. All you can do is modify existing properties such as colours (which I'd reccomend INIcoloredit for), cloud speed, etc. You can't make new weathertypes either. You'll need to wait for OpenMw post 1.0 in order to do any of these things.

I assumed Pepe mostly meant changing the R/G/B numbers.

But yeah, more clarity on what you're attempting would help

Yes let me elaborate better....if I can.

I want to be able to make double weather conditions (so it seems more randomised) to yes make different color and wind speed and such so one thunderstorm is the regular morrowind version and another thunderstorm thats more violent then the regular thunderstorm with stronger wind and more rain. Can I do that?

Unfortunately, no. As I said you can't add new weathertypes. You'll have to wait until OpenMw to do that.