unless you have the newest firmware, there is a bit of a difference in the card slots.

the one under the battery door is considered the internal card slot, and may not be hot swappable, i've never tried. the one on the bottom of the device is considered the removable card slot, and is definitely hot swappable.

with the prior firmware, many had issues where the removable card slot wound up killing the card in it (usually an SDHC card which are 4 GB and larger). some folks did have trouble with the internal card slot doing the same thing, but i dont think there were as many cases.

i dont believe the device handles one card slot better than the other, in terms of access speeds or anything like that.