Regardless of the file system, Windows NT uses cluster size (allocation unit) when organizing your hard disk. An Allocation unit represents the smallest amount of disk space used for a file. If allocation unit was 8192 bytes, on average each file would waste 4096 bytes. The average amount of wasted space on a partition is (Allocation Unit / 2) * (Number of files).

When formatting a disk, without the /A: (Allocation Unit) switch, the following default Allocation Unit sizes are used (assuming a standard 512 byte physical sector size):

NTFS

 Partition Size (MB)(low)   Partition Size (MB)(high)   Allocation Unit   Sectors 
 1   512   512 bytes   1 
 513   1024   1024 bytes   2 
 1025   2048   2048 bytes   4 
 2049   2**64   4096 bytes   8 

FAT-16
 Partition Size (MB)(low)   Partition Size (MB)(high)   Allocation Unit   Sectors 
 1   15   4KB (FAT-12)   8 
 16   127   2K   4 
 128   255   4KB   8 
 256   511   8KB   16 
 512   1023   16KB   32 
 1024   2047   32KB   64 
 2048   4095   64KB   128 
 4096   8191   128KB   256 
 8192   16384   256KB   512 

On NTFS partitions, a MFT (Master File Table) entry takes 1024 bytes, so using 512 bytes Allocation Units practically guarantees fragmentation of the MFT. Unfortuneatly, CONVERT, uses 512 bytes Allocation Units. A CONVERT is also used when you install and choose NTFS, unless the partition is preformated as NTFS.

Preformatting with NTFS requires one of the following:

1. Multiple disk drives.
2. Multiple partitions.
3. Another Windows NT system that can mount your drive.

How to install with multiple drives (or partitions).

1. Install a trash copy of Windows NT on drive 1 as FAT. I partition it as ~500MB so I can do the install.
2. Format the 2nd drive.
3. Install a maintenance (emergency) copy of Windows NT on the 2nd drive into NTmaint.
4. From the maintenance install, use Disk Administrator to repartition drive 1 as 1 partition.
5. Format the 1st drive.
6. Install your primary Windows NT on the first drive.
7. Edit C:\boot.ini and add the maintenance install. See tip 055 or tip 286.
8. Create a boot floppy.