If you are using a General Contractor to oversee the construction process, they should be the ones working with the city to obtain your permits. I would discuss the entire process with them before you start the process. I would also make sure your payments are split up for example 1/3 down before starting, 1/3 at the halfway mark, and 1/3 at job conclusion. I would also make sure your contract with them has a completion date, AND I would have a financial penalty for every day they go over the finish date. This will encourage them to make a real effort to finish on time. Always do a walk through at the end with the general contractor and compile a punch-list of items that need to be corrected before the job is done, to make sure you are satisfied with the work. Good luck!