I suppose it depends on what programs you're 
using to make the animation and to manipulate the 
scans.
It might be a pain, but one option would be to 
scan the background separately from the cels, and 
then edit in each cel layer over the background.  
Or perhaps place the cel on the scanner bed 
first, and (if you don't mind marking your 
scanner up a bit ^^;) put a pencil mark on the 
scanner to notate where the cel was placed (so 
you could put each following cel in the same 
spot) and then lay down the background, and mark 
where a couple corners fall, similarly.  That 
would hopefully insure that both the cels and the 
background were positioned the same way each time.
Just a few ideas off the top of my head.. ^^; 
Best of luck to you in getting it done!  Sounds 
like a very fun idea.

~Mala
PS: Sorry I haven't responded to your email, 
yet.  >.< I greatly appreciate your emailing me; 
unfortunately I haven't had a chance to confirm 
the sequence number yet..  I need to go dig 
through and pull that one out..