We searched on booking.com and then booked directly with the hotel.
Hotels often jack up their prices by three times or more during Oktoberfest, so we went with a better place at over €300/night instead of a normally rock-bottom hotel that was running €150. We accepted the cost and economized elsewhere on our trip. We also rearranged things so we were there during the first week.
That second weekend is typically full of other Europeans, especially Italians. The tents are very full, so plan on getting there as early as possible to get a place at a table before the reservations start in earnest and you get kicked out.
A good site w/great info is Oktoberfest-insider.com