It all depends on what you are looking for. A general practice however is to use the DUAL INPUT mode. You can select this routing on the ROUTING page.
The Dual Input mode is a Dual Mono In /Stereo Out routing. Left In is always attached to ENGINE 1 and Right In is attached to ENGINE 2. Using this routing enables you to get two different effects with separated inputs.
Connect Aux 1 from your mixer to the Left In and Aux 2 to Right In. You now have access to two seperate effects with a common stereo Output. Set the individual preset Output volumes to achieve the correct balance of the effects.
Both engines mixed together to the stereo out of the M3000. You connect the outputs to a stereo channel of your desk or to a stereo aux return. This allows you to use two seperate stereo effects with your mixer.