I do not have a solution for your problem. I guess the proper way to handle this would be to change the screen area used by nickel. But this would need some investigations. At least, I do not yet know how to do it.
Apart from that I can think of
1) putting a large top margin to the epubs (I believe Geoffry has a patch to overwrite the epub css settings by fixed margin values.) and
2) changing the configuration settings with the help of the configuration file, instead of using nickel's menu. By the way, one can change configuration values directly on the device with the help of KSM; and one can configure KSM to use a certain screen area. I know this is not very convenient, but ...
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