You have your architect design and specify window details in the plans. Pick the correct windows for the look you want with your architect and/or builder. Your builder then follows the architectural plans to achieve the look.

Google "recessed window in stucco wall".

I recommend Grace (GCP) PERM-A-BARRIER liquid and self-adhered flashing well integrated with the wall system. Pay close attention to the sill.

Give the builder well drawn details. The folks at Grace have always been a great help to me.

Here's an example of internet results:

https://www.probuilder.com/sites/default/files/2018-08/PB0818_Recessed%20Window%20Flashing.pdf

https://gcpat.com.au/en-gb/solutions/products/perm-a-barrier-air-barrier-system/perm-a-barrier-liquid-flashing

What kind of stucco will you be using, cementitious or EIFS?

The walls are thicker and are probably masonry with real cement stucco finish. Synthetic stucco doesn't handle horizontal or even sloped sills very well.

In a 2x6 exterior wall, they often will frame a larger opening with a 2x4 flat inside the opening for the window to attach to. See 2:10 in this video, and ideally watch the whole thing to see how they recommend flashing it.

https://youtu.be/mhEVQYixZdA?feature=shared

There is nothing to prevent you from installing a continuous sill under the window thereby eliminating the major waterproofing problem.