How to apply A/R to business account to balance QB and bank balance?

Thank you for dropping by the Community, Ridgeway3. I'm here to share details about payments are processed in QuickBooks Online (QBO).

In QuickBooks Online, some factors affect the balance of your bank accounts. Among these factors are mainly your downloaded bank transactions.

The QuickBooks balance is affected by all your transactions in the register and the ones you haven't reviewed yet. While the bank balance is solely determined based on the transactions on the register. You can compare the entries entered in QBO with the bank statement from their actual bank. There may be manually entered transactions on the QBO side, causing the balances to not match.

Ensure that the payment methods used for the direct deposits are correctly linked to the appropriate bank account in QuickBooks. If needed, adjust the deposit account to ensure the funds are reflected in your business bank balance.

We have also included some articles that guide you in ensuring your accounts are categorized with your downloaded transactions in QuickBooks Online to ensure they align with your bank statement. Following the steps outlined in the article: Categorize online bank transactions in QuickBooks Online.

On top of that, I've also included this reference helpful with the resources needed while working with bank feeds and reconciling accounts: How to reconcile your accounts so they always match your bank and credit card statements?

Additionally, you can check out this article that answers the most commonly asked questions about how payment deposits work with QBO: Common questions about payments deposits in QuickBooks Online.

Let me know by posting a comment below if you need further assistance managing payment transactions in QuickBooks. I'm always here to help. Have a good one.

@Ridgeway3 

"I've matched all the direct deposits I received to the invoices that needed to be paid by putting the direct deposit into A/R. The invoices show paid but the money is not showing in my QB bank balance."

When you say "matched", do you mean that you matched your downloaded bank transactions or ???  When you download your bank transactions, you should match the deposit received to the invoice.  That creates a payment receipt that marks the invoice as paid, decreases A/R (you don't need to specify A/R anywhere), and increases your bank balance/Undeposited Funds.

"I tried changing it on the invoice to deposit to "business" but then it also added the amount to my customer accounts which messed up their current balance due."

That doesn't sound right.  There is nothing on an invoice that allows you to control a deposit.  A payment receipt (New > Receive payment) is where you specify where the funds are deposited.  A payment receipt applies the payment to an invoice and deposits those funds to your bank account (decreases A/R, increases bank account/Undeposited Funds).  It's possible those payments are sitting in Undeposited Funds and are waiting to be deposited into your bank account.