If a surface wall needs two coats and this is discovered after the first coat is applied should I charge an additional amount for the second coat since it was really hard to tell before the first coat went on?
It depends on how you bid the job and what is on the contract. If you are working by the hour then it is up to the customer to make the decision if another coat is applied. If you didn't state on the contract the number of coats that will be applied and guaranteed coverage then you are obligated to apply another coat. I'm sure friends will be understanding but if you want to open a business you will need to do what it takes to please the customer (within reason) and finish the job.
It is very important to work using a written and signed contract that explains what will be done, how it will be done and any materials that will be used. This way everybody is on the same page.