When you connect to windows, the device will show up as a media device.
Inside, you will see both storages.
I've had problems, however. I have found that transferring through the nook to an sd card is more than twice as slow as just hooking the card to an sd reader.
I've also found that it cannot take files more than 2gb.
and when trying to read files off of the sd card to the nook, it will crash often.
As far as the slowness goes.... make sure you get a fast SD card so that you can write to it more quickly. That being said it's possible that the internal memory is still faster than the card.