[Otto]

Hi, Joe, and welcome to the Shack.

It's fine to use the analog outs for calibration of your system. It also allows you to calibrate the soundcard itself, so that its measurements are precise. I also use a digital output from PC to preamp, and I do all my measurements with analog I/O.

The main goal is to get a nicely integrated sub response. I measure my mains for reference only, and I dont' play with the tone controls at all. Most of use measure our sub by itself, reduce peaks as necessary, then turn on the mains and make sure everything integrates nicely. If there is some weirdness at the crossover frequency, you can deal with it then.

Give it a go and see what you come up with. Sounds like you are on the right track. We'll be here when you get your first set of measurements. Good luck!