The surround-sound channels in a 5.1 speaker configuration are the same as the side-surround channels in a 7.1 speaker configuration. You'll lose the audio intended for the side-surround channels if you tell the receiver that they're back-surround speakers.
The best thing to do is to move the surround speakers as far to the sides as you can.
There are lots of player and receiver misconfigurations which could cause you to get only stereo sound and not surround-sound.
Does the receiver's internal Audyssey audio calibration cause sounds to come from all speakers?
If not, check the cabling to the speakers.
Make sure "bitstream" is enabled in the disc player, so you get the audio tracks as they are provided on the disc.
(PCM will only provide multi-channel audio if you use an HDMI connection. PCM over coax or optical digital can only provide two audio channels. With only two audio channels, you usually can get simulated surround sound by enabling ProLogic II in the receiver.)
Marantz SR7009 avr + MM9000 amp --> Atmos 7.1.4
Fronts=NHT 2.9+AC2, FH+TM=DefTech PM1000, LCR+TM amped