what you want to do is, plug the red and white wires into the stereo outputs because they carry sound too the amplifier, so 'out' (put) of the stereo. then plug them into the amp in the inputs because sound is coming in. on the stereo and amp the plugs should be colour coded so just match them up. on the stereo one of the outputs should be labled either 'rear' and or sub, so your rear speakers or sub should be powered off the phono leads coming from here and the sub/speaker wires coming off the amp should match depending on which phono input ( from the stereo ) channel on the amp its using.
hope this is easy enough to follow, ill pm you my instant messenger address, if you use it so if you need any more help or clarification ill be easier to track down!
