A Center channel is very much appropriate for movies. You then get most of the dialog in the Center channel. For concerts in Dolby Digital, you would get the main performer (signer or instrument player) in the Center channel.
For playing Cd's I would recommend to play it in Stereo and subwoofer shutting down other speakers (unless you can select audio modes such as Stereo or Dolby Digital 5.1). If your card enables DTS 5.1, that is best.
I see in your model's specs the following:
"Functions: Master Vol., Center Vol., Surround Vol., Subwoofer Vol., CD/VCD/DVD Mode, AC3 CH Mode, Tape Mode and TV Mode."
You already have a speaker balance control in your computer's audio panel (left and right). Your speaker application provides you with volume controls for other speakers. My sense is that you should adjust volume for your system by ear and forget distances and delays. And for your subwoofer in accordance with your own taste.
There are DVD's for Video and Audio calibration (I have Avia plus a SPL meter). But this is a little fancy for your setup.