Rufus's rational side realised that he owed much of his accelerated learning to Marcus... who was indeed living in him. It didn't take much to extrapolate that his impotency might relate directly to the apparent lack of impotency of Marcus in death. This started to bug Rufus, making him deeply regret hastily hacking off of Marcus's penis and testicles.
He rationalised that the reason he was able to get an erection when he was angry was because his other side had taken charge. And Marcus was not connected with the other side... except that Rufus had consumed his balls.