Novice interconnect question.

If buying interconnects for a system comprised of a preamp, amp and CD player which link deserves the better quality cable. Finances limit my purchas to one good pair at this time.
Always, my opinion, underline that, start with the best at the source, whatever is lost there is never again found.
What kind of system do you have? What kind of interconnect are you using now and what are you planning to buy? Without knowing any of these, it is impossible to tell what will be the best course of action.
I agree with Uru and F1- I most always put my best pair between the source and the pre - so in your case the CDP and the pre - but (always a but) once you have the new ICs and have let them settle in (100 hrs min) you should try them between the pre and the amp - sometimes it works out better...
If I understand you correctly, 
The one to interconnect will best serve you when connected between the Pre and Power Amp's.
My experience is the same as uru975 & F1's. If you're going to only buy one pair, start with the source. 
Depending on what your budget is for one good IC then start with the source to pre-amp.  If things get bottle-necked from the source the rest will be hamstrung.  If your budget is say, $300 for one pair then I would suggest doing two decent pairs of ICs from the likes of Audio Art Cables, Signal Cable or Audio Envy for that $300.  Two pairs of their budget lines will be a good starting point with minimal losses.  They all offer level up products that can be purchased at a later date and offer better performance.  Best part is they offer a money back trial period.