If they are complete new windows, w/nailing fins, best to leave this up to a pro. To save on the project, you could install and flash the windows and have a stucco expert finish the job. But it will likely require cutting out some of the stucco. Stucco is not the average DIY job. Screw that up and you could end up with thousands of $$$ in damage.
Replacement windows that fit into the existing frames, do not require any stucco rework, consider that.