Setting up a 501 c 3 and will be requiring dues. How does payments made via QB work: does the money go directly to a bank account and is there a charge?

I can share some information about payments in QuickBooks Online (QBO), @aspro-reps. 

You can subscribe to a  QuickBooks Payments account to accept and take customer payments. You can accept credit card, debit, and ACH bank transfers for invoices you send and sales you make from the Merchant Service Center or through your QuickBooks Online account.

After having the QuickBooks Payments account, go to your  Account and Settings. to record payments and processing fees to the correct accounts. See this article for more information: Choose where to record payments and processing fees for QuickBooks Payments.

For detailed guidance in taking and processing customer payments, read this article: Take and process payments with QuickBooks Payments.

Your first set of payments will be deposited within 5 business days. It can take some time since we’re still setting up your account. After that, it'll be deposited into your bank account much faster.

For next-day deposits in QuickBooks Online (QBO), those payments that you’ve processed before 3 PM PT, that’ll be deposited in your bank account the next business day. For payments after 3 PM PT, that’ll be deposited in two business days.

If you don’t have the next-day deposit, payments before 3 pm PT, they should be in your bank account in 2 business days. If you process payments after 3 pm PT, we'll start the deposit the following business day.

Check this article for more information: Find out when QuickBooks Payments deposits customer payments. 

Keep in touch if you need more help or follow-up questions about payments and or anything else. I've got you covered and am always happy to assist you. Have a great rest of the day!