Sounds better on your iPod because the headphones are lower quality than your receiver/speakers and can hide these deficiencies.
A better system will not hide the faults of low quality recordings and compressed music.
In order to get bass from your 5.1 system you need to set all your speakers as small so that the subwoofer handles on the lower frequencies. MP3's don't have a dedicated .1 channel for the sub. then chose Dolby PLII or DTS:Neo 6 or even All Channel Stereo or whatever Onkyo calls it.