In Australia, the book store chains aren't that good for Indy novels and comics. When KOTCS came out, they did supply all the literature merchandise, but certain comics and books either took a long time to reach the shelf or they had to be on special order.
At the end of the day, the comic store in the city became the best place to go. They had everything in the one place and soonest. There's also an independent bookstore I go to in the city, which has the best and shortest order wait in my end of town- 2 weeks! Also reasonably priced and only needing a 5 dollar deposit.
I know that Borders are probably the best out of the chain stores here (and I think they have Borders in the States?).