i was watching horsepower tv.. and they recommended to do the following...
Bolt the flange onto the head, using a washer sandwiched between the head and flange, and another washer for the nut/bolt.
Tac weld your first tubing onto the flange
Tac weld all the bends, the collector etc
Cut/Break the tac welds off the flange from the new manifold
Weld together all of your bends and the collector
Place the manifold back onto the flange and weld efficiently, allowing enough time to allow the manifold to cool. Also keep the flange bolted tightly on the head, to prevent warping