you don't need external programs to prepare.
The combination of PDF-Mode's with zoom and margin-cut-functions is the most flexible, i know for professional reading on Pearl-e-ink device.
e.g. to read 3 columns you can combine : {Paper-Mode, 300%Zoom, automatic magin-cut} but you are free to choose, instead of 300% Zoom you could use the stylus to draw a Zoom-Rectangle the column-PDF-area to zoom in. The Paper-Mode navigate correctly thru columns with the Page-Turn Button.
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