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There is no magic formula for this. The defaults do for most conversions, but depending on both the source format and the quality of the source format you may need to make tweaks for individual books.
On the iPad my favourite epub readers are iBooks (which has excellent Calibre integration) and QuickReader (MegaReader) which integrates with the Calibre Content Server. I have given up on Stanza as it appears to have been abandoned in terms of any further development and support since Amazon took over LexCycle (the Stanza authors).
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