Thanks for the responses. I had actually tried setting the margins, but it didn't have an effect for the regular epubs I tried, and it was sub-optimal for the Kobo epubs. After reading tshering's comment I realised I hadn't actually updated the firmware since just after I bought it, so the firmware update got it to recognise the margin settings for regular epubs, that is until I tried davidfor's suggestion which works great for Kobo epubs, but for my regular ones I've loaded it stayed on the previously set margin settings. After a little poking around and I discover a reference to margins in the .kobo/KoboReader.sqlite file, but editing the values in there, which is per book and for some reason only had three books listed in the "content_settings" section of the database, anyway after editing the margins for those books, it ignores them completely. My next step has been to delete that sqlite database in the hope it will generate a new one, it is currently "processing content" after a reboot, so I'll get to bed and have another look at it in the morning. Perhaps I'll be able to do something with the margin settings for my epubs in Calibre.
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