our company uses AMEX as well and the RR number never makes it through. I have to place a special note in the comments section of my reservation to have it added manually by an AMEX rep and it's a 50/50 chance if they do it.

as far as special lines, i would hope they do add some priority line especially at the D gates since those are all WN. I'd think A-list, Business Select, and perhaps award reservation tickets should qualify.

For the check-in, they could do the same, but for now I generally just pay a few bucks to the skycap to get them checked in if the lines inside are too long. Especially in summer, everyone goes inside and the skycap line is generally just 2-3 people deep.