Yes, when using the CD analog input in bypass mode with front speakers set to "small," you would send a full-range signal to the sub.

The Model 990 uses a 96kHz 24-bit ADC chip, so the audio bit rate and sample rate will be 96kHz/24bit when using the 7.1 analog input. The DAC chip is 192kHz, 24-bit, so that bit rate and sample rate will remain at least 96/24 throughout the 990's digital domain. The 990 may even upsample to 192kHz, although I'm not real sure about that - the specs note that PCM is upsampled, but that could relate only to stereo PCM (received directly via optical or coaxial). Technically, TrueHD supports 192kHz for up to six channels (eight channels is limited to 96kHz), but I don't think anybody's actually used that capability. I know there are a few 96kHz/24-bit Blu-ray discs out there, but most are 48kHz/24-bit. That means the sample rate being used within the 990 will be better than that used originally in most cases, and in a few cases will merely be the same. Certainly not lower. Let your ears give it a try, see what you think. It seems counter-intuitive, but I think you owe it to yourself to give it a whirl before you invest too much time and effort into trying to work around the A/D/A conversion.