How should I deduct an amount from an employee's paycheck, due to the fact that I have already paid that portion of it earlier via another method?

I'll make sure you get the help you need, moshe8.

You can write a manual check for an employee. You'll just need to know the Net amount and the taxes to be withheld to manually calculate the gross wages.

Here's an article to learn more about calculating gross wages in QuickBooks Online: Calculate gross wages.

To write a check:

1. Go to the +New icon.
2. Under Vendors section, select Check
3. Under Payee, select the employee you want to pay on Friday.
4. Enter the necessary information.
5. Click Save and close.

Once done, you'll need to manually record and track the taxes as Journal Entries.

Here's how:

1. Get your employees' payroll pay stubs or a payroll report from your payroll service.
2. Click the + New icon.
3. Select Journal Entry.
4. Under the Journal date, enter the paycheck date.
5. If you want to track the paycheck number, enter it in the Journal no. field.

For a complete guide about entering manual checks in QuickBooks Online, check out this article: Manually enter payroll paychecks in QuickBooks Online.

You'll also want to run a report for Check Detail if you wish to review the check you created. Here’s how to run the report:

1. Click Reports on the left navigation pane.
2. In the Go to report search field, type in Check Detail.
3. Select the Customize button at the upper right corner.
4. Choose the Filter section, select Check Printed. Then, click the dropdown arrow and click the Printed option.
5. Click Run report.

Since you're working with payroll, you might want to check this article. This provides links about payroll task in QBO: QuickBooks Payroll help article hub

You know where to go if you have other questions running payroll. I'll be here to answer them for you. Have a wonderful day ahead.