Rent a dumpster from a waste hauling service and have it positioned a few feet away from the house when delivered. Nail a tarp to the edge of the roof and then tie the other end to the dumpster with bungee cords. This will create a chute and catch for any loose debris.
Unfasten the flashing with a pry bar or nail puller, if applicable. Put the flashing aside for latter re-installation. Take up any other fixtures from the roof such as pipes and electrical masts. The old flat roof must be free of any fixtures and obstructions.
Go the corner of the roof furthest from the dumpster and tarp chute. Begin to take up the old asphalt paper or shingles with a roofing shovel. Place the shovel spade between the roof and roofing material, the pry upward to begin. Once you have a small section up, the rest will go a little easier but still require hard labor. Push the old roofing toward the dumpster and chute as you take it up. Proceed across the roof toward the dumpster. If you cannot pull it up with a shovel, try a shingle ripper.
Cut into the foam insulation with a utility knife at the same corner in which you started removing the old flat roofing. The cut should be about twice the size of the roofing shovel's spade. Sink the roofing shovel into the foam insulation and pry up. Follow the same path as you did when taking up the flat roofing.
Pull up any remaining nails with a nail puller, pry bar or claw hammer. Sweep the entire roof with a push broom, going from the corner farthest away from the dumpster toward the tarp chute. Sweep the roof clean to install new roofing.