It is essential that the roofing contractor you choose be covered properly by insurance. Liability with sufficient coverage and Workers Compensation. Ask them to show you written proof and make copies for your records. Accidents do happen and you can be held liable for thousands of dollars in damages.
Make sure your contractor is registered with the city and he has drawn all the proper building permits for your project. No permits results in fines directed to the building owner.
Once you decide on the proper roof system and manufacturer for the new roof on your building, contract the supplier or the material manufacturer to see if the contractor is a licensed applicator for that specific roof system. A little investigation could prevent hold ups in getting your new roof manufacturers warranty.