Please don't buy the Bose if you want to take full advantage of your pre-wired house and the Onkyo receiver. For the same money, you can get a much better sound from other speakers.
All I ask is that, when you go looking at speakers, compare the specs. Most companies will tell you they have a frequency response of (for example) 55Hz to 20KHz and a sensitivity of 88 or 90 or 92 dB. Ask whoever you are buying your speakers from to tell you what the Bose specs are. Don't let them off the hook, nail them down for the specs. They will, in the end, tell you they don't know because Bose doesn't publish them.
I'll make it easy on you. Here's the link to Bose's very own website. There's absolutely no information there as to how the speakers will perform.
http://www.bose.com/controller;jsessionid=C9T9PzlBS6tgZynKDK1H9JhQL2Z98mB12NgFpSQjP2MpFdpWRzvn!-1553042229!2020971023?event=VIEW_PRODUCT_PAGE_EVENT&product=am10_surround_inthebox&linksource=productnav_txt_inthebox&pageName=/home_entertainment/theater/systems/surround/am10/index.jsp
Ferrari will tell you how many horsepower their car has. Dell will tell you how many gigahertz their computer is. Onkyo will give you a watts, frequency, and noise level. Why not Bose ?
If you want a cube type system, look at these which are non-proprietary and easily expandable or upgradeable.
http://ww3.onecall.com/PID_25552.htm
http://www.crutchfield.com/S-zWel67FNlSo/cgi-bin/ProdView.asp?wm=fp&I=107RM20&g=12700
http://www.av123.com/products_product.php?section=speakers&product=60.1
or go here:
www.accessories4less.com and follow the links to the Canton LE125 package, the Mordaunt-Short MS300 package, or even the Fosgate AR 5.1 package
any of these will get you better quality sound than the Bose for very similar prices. I'm sure other people will have any number of other recommendations.
Now as to the wires, the two hanging from the roof are undoubtedly the rear surround speaker wires. the front three: probably two are the feeds for the rear surrounds. the third might be for a sixth speaker if it's bare wire (you might see if there is a connection in the ceiling near the very far back wall) or if it is an RCA jack, it might be for the subwoofer.