how to shingle below gable or dormer?

year ago we had leak in flashing near dormer and handy man supposedly fixed it and redid flashing in front of another dormer. Now both leak and when I checked I see about 8 nails in the shingles in front of each
dormer. they had sealant on top of them but most is gone now. The questions should any nails be exposed there. Should the first shingles not be cemented down when you restart the shingles below the dormer and windows? We have roofer coming today but want to know what to expect.
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normally, a roofer would have exposed nails in a place like that covered with a dab of tar. i'd guess a more likely source of a leak is the flashing. it should be tucked under the siding. did your handyman do this?
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