I would recommend first reading the reference documentation that is included
with the source code.
Online at:

Next, your scanned files should be named sequentially in the form  
"frame_0001.pnm", "frame_0002.pnm", "frame_0003.pnm", etc. The "frame"  
part can be different, and the extension should match the filetype.  
The numbering should be consecutive with no gaps.

Once your scanned files are named properly, you should open up the  
first one in GIMP, then perform a "Video->Frames convert"; specifying  
an extension of ".xcf" (you can change the basename and/or the  
directory path should you wish). You should then close your PNM image  
window and work with the copy.

Yes, you MUST use XCF format for onion-skinning to function properly.  
Using XCF is also necessary for other useful GAP functionality  
(masking, selections, etc).

> As I've mentioned above, I'd like to be able to do two things:
> 1. Place one drawing over another and see the bottom drawing through the
>    top drawing so I can lasso stuff in the top drawing and 'register' it
>    with the bottom drawing.
Use the following Onionskin settings...

Reference Mode: Normal
Onionskin Layers: 1
Frame Reference: -1
Stack Position: 0 [From Top]
Opacity: 50%  100%
Select Mode: All visible
"Auto create after load" & "Auto delete before save" should both be checked.
All other settings should use their defaults.

> 2. Place two 'key frame' drawings beneath the top drawing, and be able
>    to do an 'in-between' drawing on the page on top, seeing both the
>    bottom drawings through the top page.

Alter the above settings as follows...

Reference Mode: Bidirectional (double)
Onionskin Layers: 2

This will result in the onion layers appearing ABOVE your frame layer  
(not underneath it as you specified). This is, in my opinion,  
preferable so that you don't have to adjust the opacity of your frame  
layer to see the previous and next frame layers.

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