When framing cels with layers, what you want to do
is put a spacer between each layer.  Cut the
spacer (mat board) for each layer so that there
is a hole as big as the painted area of the cel
(or bigger) with some room around the unpainted
edges to tape (with archival tape) the layer to
the spacer.

Then, you stack up each layer (with its spacer)
to get it to align.  You also want to do this
between the bottom layer and the bg (whether
production or what) so that the bottom layer
doesn't stick to it.

With this set up, the painted areas of the cel
layers aren't touching anything so they can't
stick.  Also, it gives depth to your cels due
to the slight (usually 1/16") seperation between
the layers.

When storing cels without layers, I either store
them seperately if full layers or if they are
just partial layers (such as mouths), I cut a
small piece of a bag and put it behind the painted
area.