The only true way to tell is by looking at the 
timing sheet for the sequence. That says which 
frames were filmed together and at what times.  
Depending on the sequence, there could be 
multiple correct pairings for a single cel.

Since I happen to have a timing sheet and scanner 
both sitting right at my elbow, you can take a 
look at one (scanned in part to be able to show 
it large enough to read):



You can see it has columns for the different 
layers (A, B, C, and D in this case). For this 
set, the D layer is a character's mouth moving, 
so you can see that the D layers are reused as 
the mouth opens and closes. Notice also the 
notation under the A and C layer columns. In this 
set, the A layer is an A1end, and the character 
on the C layer isn't on the screen when the 
sequence begins.

It's also possible for a sequence to have more 
than one timing sheet if it was used as more than 
one cut, but yet wasn't a bank sequence. The 
Angelic Layer douga sequence I recently sold on 
Ebay had three different timing sheets. Each 
later sequence had Hikaru moving in better time 
with Wizard as they danced more, so different 
layers were paired together in each one. Also, 
each time the sequence was reused, a different 
starting point was chosen. (In one cut, the A5 
frame was used as the first -- not the A1.)

But I don't have many timing sheets and don't 
know everything about them. . . So if you have 
more questions, you'd probably have to ask 
someone else. ^_^;;

All that said, if you have a quality copy of the 
film that you can frame advance and time to spend 
staring at it, you can probably guess the pairings
with some accuracy.

Many Sharp Smiles,
--Drac