If Apple does the same thing as last year, you won't have to worry.
If you pre-order online to have it shipped to you, during the ordering process, it'll notify you if there are any problems.
If you reserve an iPhone for store pick-up, you'll have the option of doing the "Start at home" process, which speeds things up in the store by having you do a lot of your AT&T account stuff online, before you walk into the store. Again, if there are any problems, it'll notify you before you get to the store.
As long as your phone is IRU (in your name, not your company's), a FAN shouldn't cause an issue. But that's not to say that on launch day, Apple's communications with AT&T won't melt down, causing problems to people with FANs. Who knows about random crap that might happen?! But in general, it's not an issue to upgrade with a FAN on your account.