Quick Answers

みどりの窓口 and Narita Airport's self-service machine. (Narita Only)

Railway/Railroad/Train station and Convenience stores. I have only been to Family Mart to charge the Suica card, so I am confident that Family Mart will be able to do it. I wonder whether other convenience stores can charge the Suica card.

No. Not really. Even if someone tells you to be able to speak a lot of Japanese. But in fact, if you reach the N3 level, there is no problem. But if you are not sure, you can read this blog . This blog introduces how to work in Family Mart. 

Yes, you can. The steps used in other stores are: Launching FamiPay App. Tap the 「ファミリーマート以外で使う」 button. Have the clerk scan the barcode. That's all. But I must say, you can't pay separately. You can only choose one payment method.  At Family Mart, you can use two payment methods (Famipay+Cash) to pay, especially when your balance of Famipay is insufficient. You can check the link below for details. References: ファミペイなのにローソンOK！使える店・メリット・始め方を解説！