Yet another answer

Quick version: doing a "format c:" does NOT affect the D: drive at all.

Once you've partitioned your HD, each partition gets formatted separately. You can format your C: partition and leave your D: partition unformatted for a while. If D: is already formatted and has data on it, you can format (or reformat) C: without affecting the D: partition.

What I usually do with a completely blank drive is create 2 partitions and format the first one (drive C. When you are using fdisk to create partitions, don't forget to use option 2 to set the active partition. Then I install Win98 on C and after that's done, I will format D from within Windows. It takes a lot longer to format a partition in DOS or with a startup disk (by typing "format D:") than to format from within Explorer (by right clicking on the D: drive, then choosing "Format").