The real answer is, it depends. Many homeowners choose to do an entire project all at once. But this is sometimes cost-prohibitive. Changing a few or even just a single window at a time will increase labour costs over time. But, the immediate cost is obviously much lower.
If this is the route you are taking, make sure to choose simple designs that will be easy to match in the future. Like most things in the renovation business, new designs and technology frequently replace last year’s models. Make sure that you don’t put yourself in the position of having to choose new windows that don’t match or having to replace a perfectly good window.