I guess I'm not sure I understand your question, so here are multiple responses:
1. Yes, if you are talking about the digital output from a CD player, you can run it to the DEQ, do the equalization, then take the digital out to your receiver and let it do it's thing, including Pro Logic II, DTS Neo 6, or whatever kind of surround processing it will do on a 2-channel signal
2. You could take the multi channel analog output from a receiver or processors pre-outs, run it to the DEQ's analog inputs, and do your EQ with multiple DEQs to handle the multiple channels. This has the disadvantage of multiple D/A - A/D conversions, which likely will reduce transparency - the DEQ's strength is in the digital domain, not in the A/D and D/A conversions.