Are you using the On screen display? I think the manual is written to assume you are. Without it it could be much more difficult to set the system up. If you have a computer screen which inputs HDMI or DVI you can use that if you don't intend to do video. Once the OSD is on, go to the speaker setup menu and make sure the surround mode is selected as 5.1. Then go to the speaker calibration screen and see if the system sees all of your speakers. Use the test tone to calibrate the system.
_________________________
Music system
Model 990/7500/Magnepan 1.6 QRs/Technics SL1200 MK2/Aperion S-12 Subwoofer/OWA3/Sony NS75H DVD
APC H15 Power Conditioner

TV System
Large Advent Loudspeakers/ Polk center/Monoprice surrounds/Panasonic Viera 42 inch/Onkyo HT-RC260/Sony BDP S590/Directv


Home Theater System
Onkyo PR-SC886/Outlaw 7125 Klipsch RF-82 L/R,RC-62 center, RB-35 SR/SL, BENQ HT1075, Outlaw LFM1-EX/OPPO BDP-83/Directv
Harmony ONE
Blue Jeans and Monoprice interconnects
APC H15 Power Conditioner