I was able to preorder a 6 (64gb) from AT&T at about 3:10AM and then I went ahead and preordered from Apple at 3:50AM when it finally decided to work. It's for the same line and I received confirmation emails for both of them.
So AT&T will automatically cancel my order from them? Is it possible to get two iPhones for the same line?
I basically did the same thing and had proper confirm e-mails for everything as well. I had a line (2 lines) with an upgrade, the Apple Store was not working and this was before the App started working so I ordered right at 3:02AM EST from AT&T for a 6 Space Grey 128GB. The other line I decided to wait and I got the store iPad app to work at 3:40AM EST or so and placed an order for the second line.
When the online Apple Store (not app) came to life again at like 5AM EST, I noticed that I could still upgrade that line that I had placed a preorder at AT&T with. I checked Apple.com's "Upgrade Eligibility" tool and it confirmed this. The system on AT&T's side showed "processing" for my order, and I had a cancel option as well. My ATT account on AT&T's website even showed the line still upgrade eligible but showed the other line I had used the Apple Store iPad app to order as used/not eligible.
So I submitted a cancel request that they said I would get an e-mail for with AT&T, placed an order via Apple.com when it came up about 5AM, and I got an e-mail very soon after stating the order was auto-canceled at AT&T because it was already taken. I did submit a cancel request right before on ATT to be safe, but I could see that it was the Apple Store order of the same line that "kicked" the AT&T one out. The auto cancel e-mail stated that the line was no longer upgrade eligible (I wonder why

). Now that line shows as proper no upgrade as it should after placing it again with Apple too
So
tl;dr - if you can still use an upgrade on Apple's Store and have a preorder with AT&T that hasn't processed to the point of showing that line as already used you can place an order with Apple if the shipping times are same/better and it will cancel the order on AT&T's side.
I think AT&T takes about a day or so at least to update their system (maybe intentionally for people like me who place an order with

directly and have a pending preorder on the AT&T site as well). Makes sense as they have less stock than Apple directly and probably would defer that to Apple if they can. It's the same price/customer anyway and they don't have to deal with much. Decent business practice I suppose
