Where to put the better cable.

Try both ways, but if the lower "quality" (whatever that means) cable is really junk than you're better off NOT using it at all, and at least substituting a known inexpensive reference IC for comparisons. An easy wnner here is the $20 Canare StarQuad mic cable the pro recording engineers use. Try TWO of them, substituting your "better" cable in each place sequentially. Try to have a buddy help you for a single-blind setup, so you don't confuse cost with "quality", as you put it. Cheers.

Timo is correct. It doesn't really matter where you put it and it will always be your weakest link.
IMHO, always use the cleanest, best imaging, sound stage, and full freq response on your source ( Pretty much the best cable you can get ) and swap around the preamp to amp cable for your listening preference.
Remember, if it sounds bad from the source then it will just get amplify to a greater degree from preamp to amp.

Everyone makes good points. Yes, ultimately it comes down to what sounds better to my ear. Just wanted some opinions. Thanks everyone!

For those curious about the details:
Simaudio Moon Nova
Harmonic Technology Magic Link RCA
Simaudio Moon P5
Harmonic Technology ProSilway II RCA
Simaudio Moon w6

And, yes, I know, I would be better served using XLR. Will do that when the budget allows.

RLW

You will end up with them where they sound the best, but if the question were asked, and the results could never be altered I would agree with Elizabeth.

Always get the most signal off of your source. No great piece of gear will add what wasn't obtained from the CD in the first place.

My mode of upgrading is always to start at the source and move back to the speakers.

Interesting thread and comments. Elizabeth's comment would be my first choice but time after time, I have found the most crucial cable link in the system is between line stage and amp. I have run a mixture of Cardas Golden Cross, SilverAudio, MIT 350 and NBS Statement. At one time I even used a cheapo pair of Belden. With the NBS being 100x the cost of the Belden, the Belden was still quite good between the phono and line stages at the time (ARC PH2->ARC LS5III) but the Belden was absolutely terrible between the LS5 and amp (VT130). All of the harmonic richness and 3D of the system was gone with a mediocre cable here and yet from the phono stage, it was mighty good! It is not always about resolution or "best cable to the top of the chain". I think it has as much to do with the cable interface between the output and input links.

Over time I switched to NBS in all links, each time making an improvement in system performance, but still trying the Belden from the phono stage to line stage, now Aesthetix Io -> BAT 31SE, shows quite a decent link....but even more so a musical disaster from line to amp. The second most critical link from my experience is the tonearm cable and then 3rd, from DAC to line stage. I too tend to start with what common sense would indicate, but my ears often tell me something very different. So the only way is to try for yourself.