The -12 is the max headroom the receiver has for level adjustment to bring your speakers to reference level. The quickest fix is to adjust it manually to 75 dB when measured using the internal test noise in your receiver, using a SPL meter. Alternatively you could add inline attenuators to the speaker channels to bring them down and re-run calibration.
The out of phase warning is just advice to double check wiring, if correct this warning can be completely ignored. (It happens due to in-room acoustics or because the speaker manufacturer purposefully made it that way).
Also, for Mic input; the MultEQ Pro software has an instruction box in the lower left hand side that will say the input place for the receiver, it is important not to plug the microphone in before it states this in the software as plugging it in early could cause speaker feedback.
