It's OK and something I knew from the beginning.
Basically its like when folks have different friends/family members switching out during the course of a reservation. We are listed on the reservation so Magical Express and checking in separately from the lead guest won't be an issue.
I have already thought about the bedding and will certainly have clean sheets to sleep on. It's a great point.
Thanks everyone for all the feedback

Looks like I will be OK with just asking for keycards and we will be just fine.