Connecting the player via USB will bypass any of the processing done on the player - the player will just choose the song to play, the amplifier will handle the decode, post processing and amplification.
3.5mm -> RCA in will go through the player’s decode, post processing and amplification stages and again the amplifier’s post processing and amplification stages.
You’ll want to experiment which sounds best to you, trying out the various options available to you, though a purist may say that USB in to the amp will be the purest version possible.
Try both out! Personally I prefer using my ZX507 with the amp via USB in - the convenience is nice.