When marking up web pages, do I put all of the markups on the home page? For example, if I mark up my payments page, does that markup go on my home page or on my payments page?

The markup should go on the page where the thing you are describing resides. So if your company is described on the homepage, the organization markup goes there. If you are describing your contact information, then the contact point would go there, and so on. For more information on marking up pages, you can check out our getting started guide here.