I'm also a Droid newbie... and am experiencing the same issue with the battery. I hate to have to buy an extended battery and then not have my case fit.
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Depending on who the manufacturer of the battery was, and how large it is in relation to the original battery, no - an extended battery is probably NOT going to fit in your case. I believe that Motorola does make an extended battery which does not require a new battery cover, and hence will fit in whatever case your using, but it only gives an incremental boost to the battery, and I've never used one myself.
The larger capacity batteries - the ones that give you more bang for your buck - take up more physical space, so of course will need a larger case. I've used Seidio on my Droid 1 and Dinc. Both batteries came with a free battery cover, and Seidio sells cases designed to fit over the extended battery - somewhere in the mid-twenty dollar range from Amazon.
This is in the Incredible forum brother. Motorola doesnt make batteries for HTC phones. lol.