When I make a purchase where does. The payment come from?

From whatever source you entered when creating and setting up your iTunes/App Store/Apple ID account. Usually that would be your credit card, but could also be Apple gift cards, etc.

Your question is confusing because you posted this in the Apple Pay in Stores area.

So when you say: "When I make a purchase ...", you may mean:

• Using Apple Pay in a store. In that case, the answer is it gets paid from the credit card that is active in the Apple Pay screen when you pass your iPhone near the NFC sensor.
• Using iTunes. In this case, you posted your question in the wrong area, but Rysz's answer above would be correct.