Based on my experience, it would be cheaper if you buy directly from the seller/car owner instead of an agent. Although mas maraming hassle as you have to do all the paper works like transfer of ownership, seeking for clearance, the savings would be more than enough to compensate for the added work.
In addition, you would know the real state of the car. Paminsan minsan if you go to a second hand dealer, they already spruced up the car.