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To properly identify how you should account for fees in your books, I'd recommend working with an accounting professional. If you're in need of one, there's an awesome tool on our website called Find an ProAdvisor. All ProAdvisors listed there are QuickBooks-certified and able to provide helpful insights for driving your business's success.
You can ignore transactions by excluding them in the Banking menu.
Here's how:
When it comes to reconciling accounts, the first thing you'll want to do is review their opening balances:
As for your Undeposited Funds account, QuickBooks uses it to hold invoice payments you've received before they're deposited into a bank account. If you're not currently using it and are curious if you should, I'd recommend working with an accountant directly. They'll be able to help you identify the best process for your business.
I've also included a detailed resource about working with the Undeposited Funds account which may come in handy moving forward: Using Undeposited Funds
Please don't hesitate to send a reply if there's any additional questions. Have a lovely day!