Suica Apple Pay is exactly the same, you add money into the SF (Stored Fare) account and every transaction deducts SF until you need to add more. Suica Apple Pay differs only in that you use an Apple Pay credit card to add money to the SF account, but just like a real Suica card you can add money to Suica Apple Pay with real money. How?
JR East has been installing new “Charge” vending machines in major Tokyo area stations. Simply place your Suica Apple Pay ready iPhone 7 or Apple Watch Series 2 device in the blue reader bin, select the amount of money you want to add on the touch screen and feed some bills to start the process, The blue bin flashes red while the machine recharges Suica Apple Pay then turns blue when the transaction is complete. You also get a notification on your device. My shaky video of the process below gives you an idea.
You can also recharge Suica Apple Pay with cash at convenience stores such as Lawson that have POS terminals with the same functionality. Macgeek has a video that explains how to add Suica to iPhone 7 without a credit card with a trip to Lawson.