Can you format the drives in an extended partition with 2 different file systems? One is already formatted and is not a regular system so is not seen by Vista's explorer and the other I would format as an NTFS logical partition.
I've no idea just how you could put 2 different file systems on same partition, never heard of such a thing. If you want 2 different file systems on same drive then you'll have to make 2 different partitions, format each according to intended use. Don't use Vista yet but best guess why Vista doesn't see it is that it's probably Fat32 or below. Vista will probably not see anything less than NTFS. Same basic error when XP and/or 2k came out, would not see FAT16 or below.
You cannot format an extended partition since it has no drive-letter assigned to it -- it's simply a 'container' for a 'logical partition' (or several logical partitions). These logical partitions are assigned drive-letters and can be formatted.