what i usually do is pop in a 98se boot disk and fdisk from there, even if the os is xp. we have the same set-up of partitions, i too have c,d and e...all in ntfs.....
reformatting everything means that your also to erase to file system....i suggest that you format c partition first,..install the os...and boot it up,..and format d and e within windows. too simply put it,..yes,..you can format c,..without touching d and e.
i keep my large files in d and e,...2 days ago,...i reinstalled my os on c which was previously on fat32 and its now on ntfs...my d and e partitions were still in fat32,..so i just reformatted them within windows to ntfs. this allowed me to move files to c, before formatting d and e to ntfs.