The official, written policy is that in order to get the Annual Pass Holder rate, you must present an activated Annual Pass in order to check in.
I've heard stories that run the gamut about people not needing to show anything, some having to show a voucher, some having to show the activated pass. I've also heard that if it is required, they will allow you to check in, activate and stop back at the front desk to show the activated AP.
I too am using an annual pass, and will have a voucher. To save any embarrasment, or sticker shock, I'll just make a quick stop at Downtown Disney and activate the thing before I check in. It's not worth it to me to have to worry about whether or not they'll ask to see it.