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When I did mine I used Calibre's 'save to disk' then chose 'save only epubs' feature.
{author_sort[0]}/{author_sort}/{series}/{series_index:0>2s}. {title}
is the string I use under preferences/save to disk. It worked fine for me, but I like nested folders. I just stick the sd card into my laptop card reader and send the books straight to it.
As far as formatting the micro sd card, I don't think I even bothered! I just can't remember, sorry! And if I did, I am sure I just stuck it in my card slot on my laptop and fast formatted it there.
I hope this helps! Sorry I didn't reply sooner, been a little crazy around here!
S
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