Agree with Kyupol; individual chapters is the way to go.
For one thing, some people see a drop-off in readers on mature chapters. This isn't true of everyone, but might be something to keep in mind. Another thing, when you schedule or post a mature chapter, your series gets hidden for up to 24 hours (presumably for some kind of review?) I've had my novel go from the trending list to invisible because of it. So, flagging every chapter mature when it doesn't need to be will probably hurt your visibility.
Anyway, if you've got one or two chapters out of the whole story, it's not anything I'd worry about. I'm not sure how long your novel is set to be, but if you're looking for comparison, I've got 50-ish chapters in my own so far. Of those, I have two sexually explicit chapters, with a handful of others marked mature because of detailed descriptions of nudity.