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In general, you should know that Kindle (mobi) always use the stock Serif font (no way to change the font) and ignore page or body top and bottom margins and the left and right margins everywhere. There is a monotype font available if you use <tt> or <pre> tags. Top and bottom margins should be set at the block level (p, h1, h2, h3, blockquote, pre, etc.). You can can change the left margin using <blockquote> or, with short lines, you can use test-indentation: to cheat a bit.
When converting from calibre, you need to make sure that you have a toc, cover and text references set. For the text reference, set the title="start" (all lowercase). calibre will convert those in proper mobi references (cover, toc and where to start reading).
I would not use MobiCreator. I would use KindleGen instead as it is supported by Amazon.
In any case, Kindle Previewer from Amazon will be very helpful to test your resulting mobi.
Hope that helps.
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