The main difference between the slots is that the internal (under the battery cover) is meant not to be removed during operations as you can set swap on it.

The external card is more for being removed so the main choice is will you ever want to remove the card?

If you have a limited set of data you want to keep on the N800 all the time then put the smaller card inside. Also, when you use swap the card is not accessible from the USB cable so the smaller card inside is probably better then you can keep music and movies and such on the external card and change that data around if you like.