I have just Googled a bit and it seems there are a variety of options for using SD cards in embedded projects.
If you have used one before, did you bother with a filesystem?
It seems the easiest way is to write raw data to the card in blocks that match the native b-size (512 bytes). This is obviously much easier than trying to implement a file system on the card, but means that a PC wont be able to read it without either:
a program that has raw access to the card
a serial interface to the uC and a program that understands the data format
A lot of people do use it as raw flash without a file system.
I never did use it as a straight raw flash device, since the first project I used with one I preferred to have file access to. I've used the library that you linked to (FatFS) on several uC's and it has worked well for me.