The reason you cannot control your volume via the receiver is because your audio outs on your receiver are before your volume control. You're lucky that all your sources are analog because if you were to use a digital input (such as an optical input), it wouldn't go out that audio out.
You need some way to get your Bose eq into the signal path at line level* for it to work properly and with your current setup, that's not an option. What Adam gave you is a workaround that, while not ideal, is the only possible way to do what you want with what you have.
* Between the preamp and the power amp. That audio out you're using is before the preamp.