I'm working on SAAS project to which I just built an iOS interface. The service is not free, but the app client could be. Do I have to pay Apple when I charge the user for the service?
Only if you charge for the service through the app. Any purchase made in an app has to go through their in-app purchase system, which gives them a 30% cut. If they pay any other way (through a website for example) you're fine.