How do I delete a bank account that's linked? Also how do you choose which account money is deposited in when clients pay the invoice?

Thank you for posting here in the Community, @myrickmechanical.

I’ll guide you on how you can disconnect a bank account, and ensure that the invoice payments will go to the new account in QuickBooks Online (QBO).

Based on your statement above, you’ll want to disconnect your bank account and connect a new one. This way, QuickBooks will stop downloading transactions from that account. Nonetheless, disconnecting this won’t change the accounting data you have in your company file.

Please take note that disconnecting a bank account will delete all uncategorized transactions. If these transactions are older than 90 days, there will be no option to download them again into QuickBooks Online.

Here’s how you can disconnect a bank account:

1. Go to the Banking menu, and select the Banking tab.
2. Go to the bank account tile, and click the pencil icon to edit.
3. Select the Edit account info.
4. Tick the Disconnect this account on save, and select Save and close.

Once done, we can go to your Chart of accounts to make the account associated inactive. I’ll show you how:

1. Go to the Gear icon (⚙) and choose Chart of Accounts.
2. Look for the account that you'd like to delete.
3. Click the Action (▼) drop-down and select Make inactive.

In addition, the transactions from your previous account will still reflect on your reports. Nevertheless, these transactions are marked as deleted. If you want to get rid of these, you'll want to delete them one by one in QBO. Refer to Step 2: Delete the transactions in this article: Delete inactive transactions that appear in the chart of accounts in QuickBooks Online

On the other hand, to ensure that the invoice payments will be posted to the right account. You’ll want to make certain of the account chosen for recording an invoice payment. Let me guide you:

1. Click the + New icon, and select Receive payment.
2. Choose the customer who pays the invoice. Then, select the Payment method.
3. Choose the correct account where you want the payments to be posted from the Deposit to dropdown.
4. Checked the box for the invoice you’re recording the payment for in the Outstanding Transactions.
5. Enter the Reference no. and Memo (optional). Then, select Save and close.

I also added this article for your reference, if you want to record a partial payment from your customer.

Moreover, learn to categorize and match your online bank transactions. Afterward, you can reconcile your account to ensure your books are balanced. 

Should you need more assistance with connecting a new bank account, you can always add a reply to this post. Have a great day!