Instead of using markers, use triggers (it'll make your life easier). Place a trigger with a radius of maybe 10-20, "group" it with the helo, and set it to "unit present". Name it something like "wp1", and put "this domove getpos wp1" in the init field of the helo.
Next, in the activation field of your trigger, put "helo domove getpos wp2". Then, make a similar trigger, name it "wp2", and so on.
I did this in my Platoon Commander mission so that I could have the convoy moving down the road normally, and then make them go to a search and destroy waypoint wherever along the road the player happens to attack. Its kinda like using a switch trigger, only a little more versatile.