First of all this pertains to 1099s not to W2s.
And that's why a simple checkbox on the page you enter the 1099 info, that you can choose to ignore, would ask if want to annualize the amount. They could also put the the little question mark thingy and you could click it to explain why you might need to annualize.
Most people would click the question mark, read it one time, then ignore it for their other entries. And if they had an unusual situation they could click the checkbox and TTax would go to an interview section to ask the appropriate Questions.
