Japanese is a very flexible language. In this case, there is no exact rule, it depends what you want to emphasize. You could say "tenki wa warui desu" --> about the weather, it is bad; or "tenki ga warui desu" --> the thing that is bad is the weather! In most scenarios, you can use either particle, but pay attention to the emphasis you're giving to the words, so that your listener/ reader can correctly understand the point you're trying to get across!