I use those cards in my MTii and some of them just die. They are pretty cheap or used to be, and I always format them in the recorder. If they don't format in the recorder they get tossed. I like to format 3 and these them, and keep 2 as backups at the show "just in case" I have to pop out the one in the deck and then I have a backup ready to go.
But in answer to your original question, use the deck to format.