When viewing the Payrun, look for the "Import Payments" button near the bottom-left of the page. Click this button.
If you have multiple pay periods (ie: monthly and weekly) then you'll be asked to select which period you're importing for.
Click on the appropriate option to upload your CSV file.
You'll now be given the opportunity to map the fields from your CSV file.
As a minimum you must have the Payroll Code for each employee and an amount.
If you're paying by the day or by the hour then you can also set a field to say how many days or hours to pay for.
Once you have mapped your fields simply click the "Import Data" button and you payrun will be updated.