The man who appears in the prologue of AffC is in a lot of ways unknown. However, there are a few things to be noted, before we make any conclusions or assumptions.
- Pate (the monk in your question) is killed by this man (from now, I will call him Killer). Pate is the viewpoint character and while his death is not explicitly confirmed (he might have just fainted from his wounds), the viewpoint character of all other book prologues has died, so we can assume that Pate did too.
- Later, Samwell Tarly meets Pate, who is supposed to be dead. From this we can infer that Killer has killed Pate in order to assume his identity for some unknown purpose.
- Pate describes Killer incredibly similarly to the way Arya describes Jaqen H'ghar when he changes his face in Storm of Swords.
From 1 we can gather that Killer is a killer, obviously a rather cunning one, and that he does not really belong in Oldtown, as he is a stranger and an outsider. From 2, we can infer that Killer is most likely a Faceless Man, as he was able to assume Pate's identity. From 3, we can gather that Killer may be Jaqen H'ghar, who has gone to Oldtown for reasons which remain unknown.
While the true identity of Killer is not known or explicitly told, it can be assumed with some degree of certainty that he is a Faceless Man, perhaps Jaqen H'qhar, whose reason to be in Oldtown is important enough to kill a man and assume his identity (simply being a guest at Oldtown is not enough, he must infiltrate the Citadel).
This character is, however, not the person who leads Sam to Marwyn, although he is present (in the guise of Pate) while this is going on. The person who leads Sam to Archmaester Marwyn is Novice Alleras, who is widely believed, though not confirmed, to be Sarella Sand (a bastard daughter of Oberyn Martell) in disguise.
Pate describes Killer
He was just a man, and his face was just a face. A young man's face, ordinary, with full cheeks and the shadow of a beard. A scar showed faintly on his right cheek. He had a hooked nose, and a mat of dense black hair that curled around his ears. It was not a face Pate recognised.
A feast for Crows, Prologue, P. 17, ISBN: 978000648612-1
Arya describes the new Jaqen H'qhar
His cheeks grew fuller, his eyes closer; his nose hooked, a scar appeared on his right cheek where no scar had been before. And when he shook his head, his long straight hair, half red and half white, dissolved away to reveal a cap of tight black curls.
A Clash of Kings, Chapter 47, p. 691, ISBN:978055357990-1