Extrapolating from Furutech balanced ICs like Reference III, which cannot be reversed for obvious reasons, the filter would go at the source end, as @roxy54 said.
Furutech Nanoflux speaker cables
Are Furutech Nanoflux speaker cables directional? If they are how do you know which is the amp end and which is the speaker end? I only found one article at Positive Feedback that said the noise filter should be closer to the source but I haven't been able to find any information that would confirm that and the person who lent me his cables swears it goes the other way. I have listened, and do hear a real difference but it is unclear to me which is "better".