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i think you'll be hard-pressed to find an easy out-of-sigil-into-iBA workflow. iBA is a proprietary format which Apple has developed that's based on epub2, but doesn't allow (as far as i know) a simple import from epub.
you can, however, drag and drop html files into the open iBA document, and then restyle it from there. it seems to respect links, so footnotes etc. may still work, but i think you'd need to rebuild the navigation as well.
in the past i've found that the templates Apple provides can be profoundly difficult to alter, and the logic behind how to create a simple layout can be a bit mind-bending, so would recommend playing around with the program and the various templates with a bit of sample text/images to make sure that you don't run into a brick wall 2/3 of the way through and have to restart.
Apple's iBA forums seem pretty well trafficked, so that'll be a good resource.
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