If your stereo amp doesn't have a processor mode, most don't, you will need to connect the Main L/R pre-outs on the Onkyo to any spare line in (except phono) on the stereo amp. Then to use 5.1 you switch on both amps, select the relevant imput on your stereo amp, turn the volume up to about 12 o'clock, and then the Onkyo volume control.
If the Onkyo comes with a microphone based setup, then you can pick a volume level on the stereo amp, and the Onkyo will balance the levels as necessary, then you just use the same volume level whenever you go 5.1.
Stereo operation is as before, just don't switch on the Onkyo.