I forget if the menu shows upon the front panel display, but you might be able to navigate it without an attached display. In case it doesn't, do you have a TV or computer monitor that you could use just to set it up? A lot of computer monitors have HDMI inputs these days - just a thought.
Audyssey is really easy to use. If you have a display connected, it will walk you through it. My suggestion, at least to start - set the microphone up in your primary listening position (using a tripod is good if you have one) and then run all of the calibrations without moving the mic at all. That simplifies it for you, and it focuses the calibration on your primary spot. If you have a display hooked up, though, I think that it gives you a graphic to describe where to move the mic if you want to do that. Btw, you'll want to move off to the side and not be in the way of the speakers during the test (leaving the room is good), and try to have your music room be as quiet as possible (like, no music playing elsewhere, A/C running, and so on). Ambient noise will interfere with the calibration. It doesn't have to be totally silent, as no house will be, but try to turn off noises that you can.
After you run Audyssey, I'll bet that the low volume issue gets better.