First off, your boss sounds a like a really stand up guy. Boning his employees, pulling their hair at work, ignoring more formal communication and from the sounds of it, generally setting a nice tone at the ol' office.

Let's pretend you're an internet browser, and press the back arrow a few times.
My overall question to you is why did you get involved with this hip-shaking Michael Scott? Hooking up with someone at work, who is of equal status is problematic enough. There's the gossip, the secret googley eyes you give each other in the copy room, etc. But now, you're adding the inherent inequality of sexing with a boss; you're guaranteeing a can of spewing emotional chaos. Relationships are supposed to be built on a sense of equality and give and take, remember?

This dude is your boss; his job is to be in charge of you and tell you what to do. Your job is to acquiesce to his needs and hate on him behind his back.

I mean, was this hook up a "wow, didn't see that coming" sort of thing? An off site work dinner at Outback Steakhouse that eventually thinned out to you and him locking eyes over a plate of onion bloomers, and consummating with a Margarita infused doggie style session in his Lexus? Or was this a slow building flirtation? The seemingly inevitable conclusion of a year-long lustfest? Two adults drawn to each other and "to hell with the consequences?"

But I guess that doesn't really matter. And, I think that's the nut of it -- so to speak. Both of you said screw the consequences of screwing -- let's screw. Now the pieces are falling where they may. He may or may not confront you in respectful adult terms about this. He is bugged out, probably regretful and scared of messing with is work life. You are hurt, feel used and positively dissed. You have now experienced the hellish confusion and conflict that arises from mixing bed sheets with Excel sheets.

What now, you ask? Now, you go back to being an employee and look for sex outside the land of cubicles. Now it's time to no longer be Human Resources.