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In the old system, you upgrade didn't just automatically show up. You had to add it to your access once you got the physical card. So be patient. Sounds like your AMEX is on the way.
I was told earlier this evening by a Macy's store associate that it's best to call the number on the back of your Macy's store card if you want the AMEX b/c if you try to apply at the store the application will get thrown out or declined b/c it will think you're app-ing for the store card.
FTR, I'm basically in the same boat. Applied 3 weeks ago in person (since that's the only way they say you can do it) for an Amex. Was apparently approved on the spot for a $4K credit line, and received a temporary shopping pass. The next day I went on line and asked for a CLI on my existing Macy's card, which was bumped up to $10K. Although the site does have an "activate your new Amex" link, I've not received it yet and there's no evidence anywhere else of it being present.
I received two Hard Inquiries, one for the in-store app and one a few days later, apparently for the CLI :/ (was hoping they'd use the same).
Anyway, I guess it's wait-and-see at this point.