How do I apply a check to the customer account when the owner took out $100 from that check for his personal use.

Thank you for joining us here, @jashleyhomerepai.

To clarify, did you receive a retainer from the customer? If so, you'll have to create a liability account to track the check amount you receive from your customers.

1. Go to the Gear icon, then Chart of accounts.
2. Select New.
3. From the Account Type dropdown menu, choose Other Current Liabilities.
4. From the Detail Type dropdown menu, Trust Accounts - Liabilities.
5. Enter a Name for the account (for example, Trust Liabilities) or accept the suggested name.
6. Select an option from the When do you want to start tracking your finances from the is account in QuickBooks? dropdown list.
7. Click Save and Close.

Then, create a retainer item and associate it with the account you set up earlier.
 

1. Go to the Gear icon, then Products and services.
2. Select New.
3. From the Product/Service information panel, choose Service.
4. Enter a name for the new product or service item (for example, Retainer).
5. From the Income account  dropdown menu, select the liability account created in Step 1.
6. Select Save and close.

Once done, you can create Sales receipts for the deposits or retainers you receive.

1. Click + New.
2. Select Sales receipt.
3. Choose the customer's name from the dropdown.
4. From the Deposit to  dropdown menu, select your account this money will be kept in.
5. In the Product/Service column, select the Retainer or Deposit item you set up.
6. Enter the amount received for the retainer or deposit in the Rate or Amount column.
7. Select Save and close.

Otherwise, follow this guide if the check is an invoice payment: Record Customer Payments.

Finally, record the $100 amount the owner took out for his personal use. For the detailed steps, refer to this article: Pay for Personal Expenses from a Business Account.

When you charge a customer for the services you perform for them, you can turn the retainer into credit on an invoice and receive it like a payment. Check out this article and proceed to step 5: Record a Retainer or Deposit.

Feel free to reply below if you need further assistance with the process. We're always here to help. Have a wonderful day!

@LieraMarie_A   Where did you get that this is a retainer, and not just a regular payment from a customer.  You know, like they (the customer) are paying their bill...? 

Seems like an awful lot of unnecessary steps for an Owners Draw.