if I want to record some music to my HD (e.g. from a CD in the CD-ROM), I normally would move the slider of the mixer for AmigaAmp input to zero position and move the slider for the CD input to the desired volume position and then have the musik from the CD available at the speakers (and for HD-rec as well).
Why are you recording CD-ROM from analog output? Why not just rip the tracks in digital 1:1 form? You can use for example
disk/cdrom/cdda.