So far, in using a "Y" connector to run the two signals from the player (CD in this case) into one pre-amp input, I seem to be getting a distorted signal. How can a person combine these two channels from the player in a way that yields good, clean reproduction from the amp?
You CAN't do this. The CD player has a low output impedance if you connect the two outputs together then you are "shorting" them. You can combine CD outputs with a studio mixer (expensive as it has active circuits) or a simple resitor bridge network with 10K resistors (build your own it is very easy).
Or just buy an Analog Mixer