How do I enter a bank deposit when a customer pays with a check towards invoice and cash is kept? As in, $100 paid, $50 deposited in bank, and $50 kept in cash.

I can help you with recording invoice payments, @artisanhkb-gmail. 

You can process receive payment for that invoice twice. First, deposit it to your Undeposited Funds account. Second, put the money directly into an account.

Here's how:

1. Click the + New button and select Receive payment.
2. Enter all the information needed. 
3. From the Deposit to dropdown, select the account you put the payment into. Tip: You can put the money directly into an account, like your checking account, or select the Undeposited Funds account. 
4. In the Amount received field, enter the amount paid. 
5. Select Save and close once done. 

The amount that you've added to the Undeposited Funds account can now be found in the Select the payments included in this deposit section on your Bank deposit page. Follow the steps below on how to deposit it in your bank account:

1. Go to the + New button and select Bank Deposit.
2. From the Account dropdown, choose the account you want to put the money into.
3. Select the checkbox for each transaction you want to combine from the Select the payments included in this deposit section.
4. Enter all the information needed.
5. Click Save and close or Save and new once you're done.

Check out this article for more information about processing a payment from a customer: Record invoice payments in QuickBooks Online.

Then, see this article: How to Record Bank Deposits in QuickBooks Online for detailed guidance on how to receive payment into Undeposited funds and add it as a bank deposit. 

Once done, you can Customer Balance Summary report to check the remaining balance for your customers. See this article: Customize reports in QuickBooks Online to help you get the most out of this report. 

I'm always here if you need more help in recording your invoice payments and or anything else. Let me know by leaving a reply below. Keep safe and have a wonderful day!