How to record this type of complicated sales transaction?

 I'm here to help you record this sales transaction, @userasbajaj001.

You can start creating a bank deposit for the income and tax you've collected. Then transfer them to your BOFA account so you can easily match them.

Here's how:

1. Click the + New icon, then choose Bank deposit. 
2. On the Account section, choose a bank account where you want to deposit the amount.
3. Go to the Add funds to this deposit section.
4. In the first line enter the $900 as Income account.
5. In the second line enter -100 as the Tax account.
6. Click on Save and close.

Once done, you can now Transfer from Square bank to a BOFA account. This way, you can match the transaction, and it will balance.

Here's how to transfer funds:

1. Click on +New.
2. On the Other column, choose Transfer.
3. Select the corresponding account on the Transfer Funds From (money came from Square) and Transfer Funds To (money to be transferred BOFA) dropdown.
4. Enter the amount being transferred in the Transfer Amount field.
5. Make sure to edit the Date, once done click Save and Close.

For detailed instruction, see the articles below:

•  Record and make Bank Deposits in QuickBooks Online
• Transfer funds between accounts

I’m adding some links below for future reference. These resources outline the complete steps on how to categorize bank transactions and reconcile them:

• Download, Match and Categorize your Bank Transactions
• Reconcile an account in QuickBooks Online

If you have any other questions or clarifications, feel free to leave them in the comments below. I'll get back to you as soon as I can. Take good care, @userasbajaj001.

Thanks for your quick response! The deposits from Square Bank to BofA happens asynchronously meaning 2-3 days of accumulated sales are transferred in bulk to BofA. Also, since the deposits are made in BofA, it automatically shows in Quickbooks. The problem is that the daily sales vs. money transferred doesn't match exactly so how to make sure that the deposits in BofA accurately matches at the end of the month. 

To expand in the components of sales: there are additional items within that sale of $1000: 

Cash (200), card (800)

Square Fees deducted from 1k income: 25

There are also discounts and refunds given making the gross sale to be 1200. 

How to organize these details so that it's tracked correctly and not duplicated?

Thanks again for your help!

Thank you for the additional information, userasbajaj001. 

If you're using online banking when adding deposits, you can just undo the deposits from the In QuickBooks tab. Once done, these transactions will be transferred to the For Review tab.

Here's how: 

1. From the left menu, click Banking.
2. Click Banking.
3. Locate the deposit transaction and click Undo.

Once you record all the transactions correctly, you can now start matching downloaded transactions. Refer to this article to learn more: Add and match downloaded banking transactions.

In addition, to lessen the total amount deposited, you can add a negative amount for the square fee in the line item when entering the bank deposit.

Let me show you how: 

1. Go to the plus icon.
2. Click Bank Deposit.
3. Add the square fee (negative amount) to the line item.
4. Click Save and close

If you have other questions in mind, post them below, and I'll make sure to get back to you. Take care!