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I know nothing about the Jetbook so accept this info FWIW until someone more knowledgeable chips in.
I think the way of customising for each particular e-reader is in the [Convert] - [Page setup] - Output profile section.
You could try setting this up for the 5" reader and convert to epub. Load the same epub onto each e-reader. Check out results.
Reset Output profile to 6" reader and convert to epub. Load the same epub onto each e-reader. Check out results.
If one Output profile looks OK on both e-readers then use that one as your default.
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