If you have purchased the optional facility that offers the ability to adjust the Class 1A at submission time, you will have an 'extra' check box when preparing and sending your submission.

If you tick this box before selecting the Prepare Submission button, you will be taken to a screen that allows you to enter additional descriptions and values to your submission. This screen allows both additional amounts to be included and/or deducted. Please note that you will need to check this box EVERY TIME you enter the prepare routine.

Enter the description (e.g. Payrolled Medical Benefits) and the extra amount that is liable to Class 1A (e.g. £12,000) and click OK. This will prepare your submission and provide a document for you to verify - you will notice that the total amount liable to Class 1A will have been increased accordingly and the new calculation performed.

This would also be displayed on the P11D(b), where you will notice the box  in section 1 will now be blank, and section 4 will be populated:

If at any stage you need to 'cancel' the alteration you have made, when going through the prepare phase, use the button in the bottom left: