the DDRC-22D seems like a typical design so I doubt it handles 2 different outputs. usually people have one or more sources to feed the same speakers, so that's the situation usually discussed. a mail to miniDSP might be more helpful for that question. about where to put it, well it's before the DAC in your case. you input a digital signal and output still a digital signal that has been processed by convolution. some gears can do more, but the basic concept is a digital process. about your concerns of altering the sound in ways you don't want, as bigshot said, the role of such a device is to alter the signal. it's based on the assumption that speakers in a specific room will not give a flat response at the listening position. and that's almost always true. you're concerned about small details while it will most likely correct much more significant stuff. how you'll subjectively feel about the change is another story. there exist many auto calibration solutions, from getting a mic(or even using a cellphone...), and using the REW and some free convolution option on a PC, to very advanced and expensive auto-calibrating stuff. it's always hard to know what we need/want.