Damn, totally forgot about that. I seem to recall Archer was embarrassed by it but apparently Pam was a great lay. Didn't his father die on that episode? If so, he might have been distraught over that so just didn't care about Pam screwing his brains out anymore.
The way it played out, Archer was embarrassed by it and yes, he told Pam that she was the best sex he's ever had ("You're like a chupacabra, but for dicks"), so he would keep sneaking off to bone her. Archer told her to not tell anyone about it and Pam later said that she is just using him for sex.
In the episode where the bang-buddy relationship begins, the former head of the KGB and potentially the father of Archer (though there are other possibilities including the head of ODIN & Buddy Rich) is killed by Barry before the DNA test can be done, so the man dies without ever knowing if that was his dad. And yes, this took place because he sneaked away to go bone Pam.
He felt guilty about it, but the fuckbuddy deal continued past this episode. Pam seemed disappointed when Archer's dead fiance Katya was brought back as a cyborg, and she even told Archer in the next episode that going for Cyber-Katya over her hurt. Also in that same episode, Archer smuggles her on board the space shuttle he is traveling in just so he can fuck her. They even have a quickie while in space.
So the way they left it, it sounded like the bang buddy deal was still going. I just rewatched the episodes again and the only other characters that know are Ray & Woodhouse.
Phew, I made that sound more complicated and serious than it really is. I would like them to explain where the stance is on that though.