Auto setup
The auto setup on your receiver should be pretty good. Most people find that the speaker distances are accurate and the volume levels are within 1 dB when comparing with the Radio Shack meter.
Your best bet would be to double check some of the speakers settings. Here is what I would recommend:
Speaker size - set all to SMALL
Crossorver - lowest frequency of your speakers, probably around 80 Hz
Sub - Yes, Sub only, not both.
PEQ - Experement with turning this off, on FLAT, etc.
If you want to tweak your video, AVIA or Digital Video Essentials are your best bet. For $40 the Radio Shack SPL meter will help you check your speaker levels and calibrate/position your sub.