Will I get a refund if I pay excess tax?

I have filed extension request with IRS. I am planning on making a payment of the tax I owe to IRS by May 17. However, I am not exactly sure yet on how much I owe. I want to err on paying more tax than I owe rather than falling short and incur penalty or late fee.  In the event I pay excess tax than I owe, will IRS refund me the money when I file my returns in October? Also, if I pay using credit card, will they chargeback to card or issue a refund to my checking account as they typically do.