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What is an example of the best way to play the overload on counterflux ? It would only cover what is on the stack right? Can you bump up the cast to overload while it is on the stack? Or is it something you must declare when you cast it?

An overload cost is an alternative cost to casting the spell.  As such, it is something you announce when you're casting the spell, and not at any other time.

You're correct, Counterflux only counters spells that are currently on the stack at the time it resolves.  Generally, this is an effective counter to use against spells with cascade, or storm copies -- or less commonly, any other situation where an opponent puts multiple spells on the stack without letting them resolve.  It can also be used to win counter wars fairly decisively.