total of 2 sets of RCA cables? For some reason i only have 1 set of RCA cables coming from my deck, and the speaker amp is only for the rear speakers... so did best buy mess up the installation???
My guess is yes if there is one set heading from the head unit toward the sub amp that send audio towards your sub amp but if their is no RCA cables connected to the speaker amp good chance it is installed incorrectly but then again best buy is quite tricky with their installation so it may be hooked up a different way i do not know about.
so you have two amps? well they could connect the two amps, so look for wires from one amp to the other, they would be signal wires like your rca's, but if there not i might be suspicious. there are probably other reasons for whats going on tho.
you should need 3 pairs of rca's (1 pair for the front 2 speakers and 1 pair for the back 2 speakers and and 1 pair for the sub amp that is only it your speaker amp is 4 channel) and your cd player will need 3 pairs of rca outputs