"It was cloudy this morning."
Yes and No.
は is used for making a topic, so you use は when you do need to make something a topic. That's it.
今日 買い物に 行きます。
I go shopping today.
(Today is just an information)
今日は パスタを 食べたい。
I want to eat pasta today.
(More precisely Talking about today, I want to eat pasta. Perhaps I usually eat rice everyday, today is special and I want to bring it up as a topic.)
You are beautiful today!
(…What? Did I use to look awful?)
ね is an agreement seeking particle but is also used to confirm a fact or a sense of "togetherness". So, yeah, it may be translated as "you are beautiful today, aren't you?" I believe it is more of a confirmation (by being flattering) of what both people would agree on, or more of a rhetorical statement.