Roofing Problem

My roof was replaced a year ago and we discovered two significant leaks after a recent rain. I should explain that we've been in a drought since the roof was replaced and this was the first significant rain since then.
The leaks were under two windows in our upstairs bedrooms that mount on the wall over our garage. I had told the roofing company to replace the flashing over the garage when they first replaced the roof. Unfortunately, they didn't do that at the time and I suspect the leak was due to that error. They came out and decided they would replace the flashing but do so by nailing the flashing over the stucco and then under the asphalt roofing shingles. They said it could be done two ways and that this would be the less destructive way and it wouldn't involve us calling out a stucco man to replace the stucco they would otherwise have to remove. More rain was due so we agreed to nailing the flashing over the stucco as long as it was a valid fix.
That was two weeks ago and now I've got some concerns. How will the flashing stop the rain that goes into the stucco from draining down behind the flashing and into our house? That seems like an obvious problem but now that its done should I paint and seal the stucco above the garage and windows to prevent this from happening?
Thanks for any help.
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