The quality of the sound from TV or mediabox is an old problem, what comes in comes out, your mediabox is probably not the best source.
I have an Onkyo amp/reciever where I distribute sound from TV (HDMI), set top box (analog), Blue-Ray (HDMI), Computer (Optical) and BG 5000 (analog). I have a BS 3000 and it was connected, but as the Onkyo is a reciever and I play my CDs on the blue-ray, I took it out and run it in a different room.
I have connected to the Onkyo preouts, BM 8000s (front), BM 4000 (center) and amp out S45s (surround), The sound from the Blue-Ray with a good quality B-R disk is espectacular. TV is depending of the source from the sender, HD with good sound is very good indeed.
2. Quality of your CDs will not decrease, and you will be able to distribute the sound through your Yamaha and fit it to surroundings and your ears.
3. Negative for the BLs is the line connection, sometimes, in a surround sound set up, watching a movie, your amp will not distribute sound to some of the speakers and the speakers goes into standby, this happens under long passes of silence or long passes of low speaking. Separate your sound and power cables as the line connection has more tendency to cause "hum".
As for using the Onkyo instead of the BS 3000, with the BS I had to use a source selector and a preamp for the BG, and no surround sound, and with the Onkyo I can change, distibute and select in or out and combine everything from one remote.
But I love listening to my BS 3000 with BLs 4000 and a good music CD, this stereo sound is kind of special and you wont be able to reproduce it with your Yamaha or any other amp, its "special".
Beosound 3000, BL 4000, BL 8000, BG 2404,BG 5000, BG CD50, Beocord 5000, BM 901, BM 2400, BM 4000, BV S45, BV 3702. There is nothing we cannot do, but a lot of things we don't want to do!!