There are quite a few plotting tools in Papyrus! If you’re still exploring, check out the Start Screen’s Learn page. I’m sure you’ll find something new in the “Worldbuilding” and “Writing” tabs.
For a short story collection, I think I’d first decide whether the stories live together while you write them, or only come together at the end.
If each story is mostly separate, you could write them as separate documents or projects, then bring them together into one finished book later.
If you’re working on them at the same time, and want to keep the whole project in one place from the beginning, you can write them as separate chapters like @alcen said, and mark them in the Navigator with colors and icons.
And for example the Thinkboard can have as many separate tabs as you want, so you don’t have to brainstorm into one big maelstrom!