You are making an incorrect assumption. If you book directly at Cathay Pacific's website as a guest, you don't need to use "Manage My Booking" to add you Qatar PC number to the booking; you simply add the number on the same booking page where you add your name and date of birth to the reservation:



I would only consider using a travel agent for such a booking if there were a substantially lower fare available through the agent, and only if the agent were known to be reliable/legitimate.