Upvote:2
The Global Distribution Systems are very complex animals. Wikipedia has an example for what you are doing here. You will get a PNR from Booking.com which contains the entire itin (flights, hotels, cars, everything) and there will be a VN PNR and a CA PNR. If the Booking.com email doesn't contain them (I do not know because I never use them for booking flights, it's typically pointless) then contact them and ask for it. Armed with those, you will be able to add your frequent flyer program either online or via phone, ask for special diet and all that jazz, your ticket might even include free seat choice. And you can always add the frequent flier numbers at check in as well.
Here is an example from a different agency (it's very old so I am no doxxing myself here):
as you can see there's a locator for the entire trip and then there's the Air Canada code, separately.