I found that you can put the regular battery cover on over the extended battery, it's slightly tight fit (the edges bulge just a tiny bit in a couple places), but if you're having trouble fitting the extended battery cover under a case it might be worth a try. I don't like the idea of having no battery cover on under my case personally, mostly for fear of dust and crap getting into the phone's internals.
Edit: Also, has anyone gotten the Seidio surface case yet? I have one on order but it was backordered so I canceled my order with Seidio and reordered it off Amazon.