Newbie question.

why are you using 2 pre-amps? if your using the pre out of your sony why bother use the other (unkown model) pre- amp, just go directly to the amp from your pre out of your sony. lastly using your Iphone as a hi rez music device into your pre- amp via the head phone jack is not getting the benefits of the higher rez files to be honest.

I didn't know apple could do Flac good to know they are finally using a better format then apple lossless imo. 
 
I can't comment on the sound quality of a sony receiver but if its up to snuff and you like it then why not just use it and sell the rest. or get a separate tuner and ditch the Sony if your separates are good.  you could easily get a used tuner for what your sony is worth...probably a better tuner IMO think vintage here. 

What i would do, knowing little of what you have. sell the Sony buy a tuner. save up and get an Audioquest red DAC (around $299 last time i checked) that will plug into your Iphone and out put that to your pre-Amp via 1/8 jack  using a 1/8 to RCA adapter (with fixed vollume). this will get you along way towards better sound. also the Audioquest red can be used directly into your head phones for great headphone listening on the go. this would be good sound for a budget and a good start. 

 

I'm using two preamps because I already have the Sony combo unit and don't want to buy a tuner or spend any more money. So it us basically just a tuner in that sense.High end stuff is a gift/loan. So, this is what I've got, just trying to work with it as such. I just thought if I could run flac files through this system using what I have then it might be worth it. If running them through the Sony would degrade the sound quality such that I might as well just use mp3 then I'll just stick with mp3.

Most of my listening where quality matters will be done via CD or phono directly into the good (AR LS16) preamp and Proceed HPA2 amp,  bypassing the Sony unit altogether.. 

So the Sony will not cause me to lose quality anywhere else. Just the radio (where I don't care what the quality is like) and then possibly with flac or mp3 files.

Sorry to be so confusing.

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ok then just plug the DAC/iphone into your Arc Pre and be done with it.

Why go through the Sony if you have the Arc Pre go through the Arc as with the other inputs. Just note you will not get all the advantages of the Flac files but it will, even through your phone, sound better then mp3. get a apple to RCA adapter and go into one of the Arc's inputs skipping the sony all together because yes it will degrade the sound as you are going through a lot more circuits. just use the sony as your tuner. 

Do you have any available open RCA inputs on the ARC pre-amp? If so, just get a 1/8" to dual RCA male cable, like the one linked here:

https://www.monoprice.com/product?p_id=5597

You can probably get one of these cables at many brick/mortar electronics store or Amazon.

You will plug the 1/8" connector into your phones headphone output, and the RCA's into any available input connector on the ARC pre-amp. This will remove the unnecessary Sony from the chain. For a couple of bucks, it's well worth a shot.