In this photo, you can see that several roofs have been installed on top of the other. This is generally not a good practice for longevity and is prone to leaking. Nails are likely not to reach the wooden decking below; even if they do, I am likely to be driven into some soft areas of wood. Exposing the entire roof deck is always the best plan.

In the photo above, you can see that a flat roof was installed over the porch stoop in the rear of the house. It appears that it was not tied incorrectly to the existing shingles, nor was it tied incorrectly to the house under the eaves. This area appears to have been having problems for a long time as the structure underneath is compromised with rot. 

Here, you can see that the decking boards beneath the shingle layers have given way to rot. Sagging is evident, and the area is very soft and spongy. Some boards will need to be replaced as the roofing process starts.