Ordered Nike+ edition from them. Used ApplePay through their app. Also charged upfront and am still waiting. I initiated a chat with them online to ask why I was charged upfront and was told it was because of using ApplePay. Seems ApplePay transactions must be charged immediately...maybe the secure token generated expires if not used within a certain timeframe? I did see the notice on their site that PayPal transactions are charged upfront, but nothing about ApplePay.
The chat agent did tell me that it would be possible for me to call in and have my ApplePay transaction refunded and then provide a credit card number for the order that would be charged when the watch ships without losing my spot in the order queue. I haven't done that though as I just don't want to risk screwing up the order. Decided to just wait it out.
EDIT: Actually, I did just decide to give them a call and make the card switch since my payment on my credit card isn't yet due and I will get the credit before it is. It was actually pretty easy to make the change. They sent me an updated receipt showing that the ApplePay was refunded and that my credit card has been added to the transaction. Interestingly, it appears that since Oct 1, B&H is now charging sales tax. Since my original order was in September, they gave a credit for the amount of the tax. I wonder if they are eating this charge or if they have a way to not pay the tax? I checked online afterwards and my order confirmation still shows the original date of order, so hopefully I did maintain my spot in line.