I would definately seperate the cel & the 
background if you can.  The reason for this is 
because sometimes the paint used for backgrounds 
can tend to seep through the cel...& leaving them 
together can cause them to end up sticking 
together in the end after storage.  Just put them 
in seperate cel bags, & then tape the cel to the 
background so they stay together even though 
they're in different bags.  Usually if it comes 
with a sketch...I keep it in the bag with the 
background...On the side that's not painted ^^'!

Just be very careful when removing the tape from 
the background...It usually has a tendency to 
take the paper with it ^^'!  If it starts to do 
that...You're better off just leaving the tape on 
the background.

Hope this helps!