It sounds like you are wanting to simply inject these HTML 5 elements as an afterthought, in order to make your document more semantic and hope that all your current styles will continue to work as is? This might not be the case, especially if you are creating an additional level of nesting in your elements.
I think in some cases these HTML 5 elements should ideally replace your generic DIV containers, as otherwise it's just adding unnecessary bloat to your page. Particularly if you are simply wrapping an HTML 5 element around one of your DIV containers.
Whether you have the <article> inside or outside the <div> shouldn't matter semantically IMHO?
...having trouble using the margin:0px css that would usually put the div to the very top of the body element...
This sounds like it might be a collapsing margins issue? With an additional element between your DIV and the BODY, the margins on the body are no longer collapsing...? Do you clear the padding/margins on the BODY element?