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I recommend running fdisk, and formatting at least the boot partition from a boot floppy.
I always use a boot floppy (or CD) for the target operating system. I do this to prevent any compatability issues between the OS, and the version of fdisk.
Then, I personally look at the cluster size chart for the file system.
I try to keep from creating a drive that is just larger than the step in clusters.
(remember, that drive size is in binary, not decimal steps 1K = 1024 bytes)
As to partitioning, I like to use multiple partitions on larger drives. This allows me to organize files for easy backup, and keeps fragmentation on the boot drive to a minimum.
For a good article on partitioning philosophy, check outwww.aumha.org