As long as you make sure to have all the .ini files with CoT in the name from the CoT download, and the vanilla from the pureweather one you will have the best from both worlds.
I do not remember if I actually copied in the latest CoT ones into the pure weather update.. I might have in which case you do not have to do anything. Also if you think it already looks nice then all the better.
At least all the weathers are in the weather list and it will all work just fine out of the box!
Hope that did not confuse too much! :)