What you describe sounds OK to me. Perhaps it helps if you know that the signals are on the three jacks. The jacks are color-coded, and the details will be in the manual of your mobo or sound card. I'll use the "typical" colors here, but check your own manual. EACH socket contains two signals. If you look closely at the male jack you plig in, each has a tip, a ring, and an outer sleeve - three contacts. On each, the Tip and Ring are the + contacts for two different signals, and the Sleeve is the common Ground for both signal circuits.
Green normally is the front left and right stereo signals. You'd probably take those to the front stereo inputs of your 2.1 amp.
Orange is usually the front center speaker and the sub-woofer signals...