So you want to be able to use the 2.1 speaker system that came with your PC in 2.1 mode and then switch over to a pair of bookshelf speakers in stereo mode connected to a seperate amp. Is that correct?
If so, then the easiest way I can suggest (I've done this) is to use a 3.5mm STEREO to Left and Right RCA cable to connect to your amplifier's inputs. This is a very common cable, with male ends. When you want to use the seperate amp with the 2 speakers in stereo mode, simply plug it into your PC headphone/ earphone jack. Typically, the PC sound card will detect the connection and automatically switch from the PC's 2.1 (SUB/SAT) setup over to the 2 channel stereo signal at the headphone/ earphone jack. Just remember to turn down the volume on the PC and keep the amp off while making the connections. Otherwise, bad things may happen to the tweeters. Turn on the amp and adjust the PC volume at the mid-point and then turn up the amp to your desired volume and then you can control volume, mute, EQ, etc... from the PC.