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Rule of thumb - don't put often-needed files on the microdrive, and you'll be fine - movies are probably the only thing that should go onto there, outside of huge files like GPS maps. Otherwise, I've found the drain is minimal, with the proper usage of the drive and programs which can cache information ahead of time, which means fewer drive accesses are required to get your data (and by doing so, reduces the power usage of the microdrive). Otherwise, if you're intending it for storage of music or programs, get the CF card instead.
Either way, the CF card WILL pull more power than the SD card will, reducing your battery life when both devices are used; that's something you won't be able to avoid, unless you keep your CF slot empty. However, you can reduce the amount of power usage if you're smart in your file allocation; put the important, most-often accessed stuff on SD or BIS, and then keep the CF free for things that aren't needed as often whether you're using microdrive or solid-state.
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