If you have room to store more portable, and are happy with a portable set-up, that would be the way to go; both practically speaking, as well as concerning cost.
Or consider a side mount, if feasible, so you can access it without climbing on the roof.
I found a place in Markham, Ontario, that sells poly panels for about $1/watt + $? shipping.
http://2solar.ca/As for wiring, I'd go with one pwm controller, mounted close to the batteries. Then hook up as many panels as needed, in parallel. Just be sure to allow for the amperage, i.e; total output in amps + at least 20%. So, if you wind up with 200w total, that will give you about 12 amps, so go with at least a 15a controller. But for a few bucks more, the solar30 comes well recommended.
http://www.ebay.com/itm/30A-12V-24V-LCD-display-Solar-Charge-Controller-Regulator-Light-and-Timer-DX-/251760210331?pt=LH_DefaultDomain_0&hash=item3a9e13f19b