May depend on the page size it was originally formatted for. If it's Japanese, don't they typically use the "B" series of paper sizes? Which means the screen ratio may not quite fit.
I don't have any actual manga -- only some graphic novels, and the screen seems more friendly to graphics originally composed to fit a page in the A4 or US Letter dimensions.
I've never had to convert any myself, so I just leave them in the zip file. But I've heard others say calibre is the way to go. Just have no experience of it myself.
(Hmmm, that probably wasn't any help at all. Sorry!)
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