The old covering comes off down to the deck. That is the point at which anything hidden becomes visible: soft or delaminated sheathing, previous repairs, penetrations that were never flashed properly. You see what we find before it gets covered up again, not afterwards.
Then underlayment, flashing at every wall, valley and penetration, and attention to how the attic ventilates. Flashing and ventilation are the two things a cheap quote quietly leaves out, and they are also the two things that determine whether the new roof performs the way it is supposed to.
The covering goes on last. It is the visible part and the part people shop on, but by then most of the decisions that matter have already been made. If you are weighing coverings, the comparison of roofing systems sets out what each one is for.
Roofing work here is permitted and inspected, and the requirements are set by whichever county your property sits in. Escambia, Santa Rosa and Okaloosa each run their own. We confirm what applies to your address before the scope is final.
This is the sequence for a full replacement. If the problem turns out to be localized, a repair may be the better spend. To check who you are dealing with first, see the Navarre shingle replacement: before, during and after. If the property is a rental, an office or anything with tenants, the commercial roofing page covers how the same approach works around an operating building.