Hi
Logitech Z906 has got the digital connection option through an optical cable. That is if you connect the toslink cable to your motherboard then you get the best sound output depending on what file are you playing. If you play a mp4 file and mkv file with dts sound encoded there will be a hell and heaven difference.
That being said you have to make sure that you are not using 3 -5 cables for individual speakers ( from mobo to z906 ) like centre, rear front subwoofer. All of these can be done by ust one toslink cable.
Now please check what mobo you have and do you have a optical output option at the back panel. If not then please buy a sound card if you wish to get the best output from the Z906.
Let me know if any queries...