Follow the guide Here to generate your mass pay file.
No follow the guide Here expelling how to mass pay your affiliates in PayPal.
Once you have paid your affiliates you can use that same exported mass pay file to upload to the system and mark those affiliates as paid.
Upload a csv file with one affiliate per line in this format:
Paypal Affiliate Email,Month,Year
For example: firstname.lastname@example.org,2,2012
This will set all the commissions for these affiliates for the month of February 2012 as “Paid”.