If the dataflyer has autoboot capabilities, you can handle the CF card like a harddrive, no need for special drivers.
However, if you want to use the CF card to exchange data with a PC, you should better use a PC file system (for example CrossDOS or FAT95) and a mountlist so that the PC can read it.
You probably won't ever exceed the number of possible write cycles of a CF card in your life. Imagine that you have to write multiple tenthousand times to each single cell of the card in order to destroy it. Even if you save and delete a million files several times you won't ever reach this amount of data.
Bye,
Thomas