Dana,
It's very hard to explain in words how to weld. You really need to see it done, at least.
You apply the flux about the time you mentioned, but you have to let the billet come up to welding heat and let it soak, as Wampus said, till the middle of the billet is as hot as the outside. No dark area or shadows. Keep fluxed.
The initial weld is where I have had trouble. Concentrate on getting the weld right, before reducing the stack very far, then draw it out for your next cut and stack. Look up everything you can on forge welding and get a mental image of what to expect when you are doing it. Or better yet, take a class. It will cut years off your learning curve. Lin