hotwire said:
You might also try and mount the conduits away from the studs so that if the drywallers miss when they nail or screw on the drywall they are less likely to hit the conduit.
I was going to say this, too. In your top and bottom plates, drill the hole for the conduit 2-3 inches from a stud. You can then pull the conduit through it, and only need to proect the top and bottom plates.
If you're using flex duct and need to, you can always use a conduit bracket in the middle of the wall (eg: the conduit starts 3" from the stud on the bottom plate, angles to the stud where the conduit bracket is, and then angles back to the top plate hole)
Two additional thoughts:
1) if you have open walls, don't run your cable through the conduit. Keep the conduit for add-on cables, and pull what you currently want through separate holes (ask yourself how many times you're going to _need_ to remove a cable that is supposed to be installed somewhere else!)
2) After the drywall is installed, test and make sure your conduit is in one piece and not spiked.
I can't tell you how many times I've heard of/seen drywall screws going into conduit, PVC plumbing, etc. If you catch it soon, you can have it redone. Typically, cutting out drywall, patching, and replacing due to an errant screw is the responsibility of the drywall firm.