If you have a motherboard with 6ch output, you would be able to continue to use all 6 speakers as separate surround sound. That would likely be your best bet if you really want the most clarity out of the system. Another thing you should look into is either getting a higher quality sound card so it outputs high enough voltage to match the amplifiers input range, or a line-driver/EQ that can do the same.
That being said, if you really want a single 3.5mm input, you're going to have to use spitters, or get a 6ch amp that only has 2ch input (Not sure about that one existing?). Amplifier input impedance is high enough that you don't really lose much if any quality from splitting the signal, but really the best way would be to actually have direct 6 channels of output going into your amp (or amps), then to the speakers.