The straight answer is do it any order you can.
Honestly I think it will depend more on the quality of the cable more than the order employed. For instance I found using Cardas Golden Ref ICs between my pre to my amps produced the biggest change for the better. Simply all around great rich tone and big sound stage with details preserved.
I would tailor your choices around the sound you want most. I used Silver Lace (pure silver) by Homegrown from my TT to phono then Millersound's clone Ultraconductor Aluminatas to pre to get the most detail from my TT. I wanted a richer fuller but detailed sound from the CD player so I used Audience Au24 from my CD player to the pre and finally Speaker cables by Jena Labs all Cu braids to my detailed speakers (Jm Labs Electra 936s).