Please describe the speaker connections to the Bose 'bass module'. Is it the type where ALL of the speaker wires connect to the bass module?
If so, you want to run all of the wires from the respective speaker terminals on the Onkyo to the bass module and then go into the setup menus on the receiver and set every channel to Large and Subwoofer = No. That is because the bass module has to do all of the xover work to send the appropriate frequencies to the little cube speakers.
The TV video connection is easy. You can use composite or s-video connections from the 'monitor out' on the back of the receiver to the same type of connection on the TV (and then change the tv input to whatever the input to which you connected is named; ie if the input on the tv is named 'video 1', change the tv input to video 1). If you have (or will buy) component video cables, you can connect from the component video out on the back of the receiver to the TV.
You need to calibrate the levels of each of the channels. 45 would be normal if the room is very large. That's about half of the range of the volume scale.