Don’t do it
I just had to say it. Avoid the whole thing altogether, if possible. It’s messy, it gets emotional, it’s awkward for you both (not to mention your other roommates -- it’s San Francisco: the walls are not that soundproof), and it can only end in heartbreak. Do you know how hard it is to find a reasonably priced apartment in this city? Don’t jeopardize the one you have. But you knew that and you did it anyway, so now what?
Have “the talk”
This isn’t your usual wait-two-weeks-to-text/see-if-anything-better-comes-along hook up. You’re going to run into your fling over coffee every morning, so you can’t ignore the situation (even though you can semi-avoid it by running to Four Barrel for a coffee from that cute barista instead). It’s gonna be awkward, but you and Roomie need to communicate early and make sure you’re on the same page. Was it a one-time mistake? Do you want to do it again and keep it casual? Are you trying to date? These are all questions that, unfortunately, need to be addressed right away. With a roommate there’s no middle ground, no game playing. You’ve gotta figure it out and you’ve gotta figure it out now.