When you're done with you match, you fill out the match report on WhosTheRef. You also need to report and cards you issued there. If you have any red cards, then you also need to email firstname.lastname@example.org within 24 hours of the end of your match.
Login to WhosTheRef.com and find your match under the Fixtures page. Next to your name, you'll see a button marked MR. Click it.
Fill out the report that pops up, including the number of each type of score, and whether or not there were injuries or disciplinary issues.
Save your report.
When finished writing your report, make sure to check the Final Version box. Otherwise, your report will never be filed.
If you had any red or yellow cards, then you'll need to report those as well. Return to the Fixtures page, and next to your name and the MR icon, click the little plus sign. It will pop up the red and yellow card icons. Click on the appropriate one, and it will open a new report form. Repeat as needed.