All of my letters were submitted in airlineapps and pilotcredentials. I have some generic references attached to the main application (airlineapps) and then each airline has an addendum. That is where I targeted pilots from within that airline. You enter the email address of who you want to submit the letter and they get a link to follow that will populate their letter into the proper place.

I have some hard copy letters of recommendation from my commander and a few others, but I haven't found a place to use them yet.