I have a client who's trying to use QB in an auto repair business and has quite a complex setup, and not in a good way. He uses Winworks to generate the initial paperwork, then has a secretary enter it in Quickbooks.
I couldn't find any modules specific to auto repair, but he needs to handle invoicing, parts ordering and inventory, and all the tidbits that go with running a shop and employees.
This sounds like a typical business setup. Most companies invoice and order parts and have inventory. If you don't understand the program enough to set all this up then get somone in that can do it for you. The QB manual covers all this, too.