For my setup, I've got a computer acting as a "jukebox" with a mini jack plugged into the "line in" on my amplifier, and that's petty much it. I haven't messed with any settings beyond that- if it sounds okay going into headphones, it sounds fine coming out of my setup.
That said, my setup is made up of older, lower-end equipment, so any minute issues there might be in the audio aren't ever going to be noticeable, and certainly not to me after working next to the blower system at the factory for all those years. If you have a setup that leans more "audiophile" then you might need to tweak your output device a bit to compensate. I'm told that TOS-Link/Optical Audio is the best for this because there's not really a way for electronic hiss to be passed by fiber optic, but I have zero experience with that on my hi-fi system, and as said before, I doubt I could discern a real difference anymore.