Planning
All of them, or just the bad ones
Doing a house in stages is a reasonable decision. It is also more expensive per window than doing it at once, and it is worth knowing by how much before choosing.
Why fewer costs more each
A crew's day is the unit of cost, not the window. Setting up, protecting floors, and cleaning down happen once whether they fit two openings or twelve. Delivery is charged the same way, and a second visit later repeats all of it.
That is why a single window rarely justifies the trip and why most contractors treat two as the point where a job starts. It is not a rule imposed on you; it is arithmetic you can check by asking for a price for two and a price for six.
When phasing is still right
When the failures are genuinely local — one fogged unit, one rotten sill on the weather side — and the rest of the house is sound.
When the budget is the constraint and the alternative is waiting two more winters with draughty windows in the rooms you live in. Do the rooms you use, on the weather side, first.
When part of the house is due for other work anyway. A window is cheapest to change while the wall is already open.
What not to phase
Matching. Windows bought two years apart in the same product line rarely match exactly — profiles change, and so do the whites. If the front elevation matters to you, do that elevation in one go.