Ouch! 512 bytes? Was the drive converted from FAT32?
If you're talking about installing Vista onto a boot / system drive (or partition) with 64 kilobyte allocation units, then I guess you might boot with a pre-install environment disc and use the format command. I don't think installing the OS onto such a partition would have any advantages at all, though.
But if you're talking about a separate data drive or partition, then just install Vista first, then use the format command from the CLI to format the target partition.
If you type
format /?
at the command line interface you'll get a summary of the switches and options that work with the command. The switch which controls file system is /FS, and the one which controls the file allocation unit size is /A.