If you are connecting the external hdd via a USB cable, make sure you use the "Safely Remove USB device" feature of windows before physical removal.
Or it might corrupt the data on the hdd.
"{Delayed Write Failed}" error message when you unplug a USB 2.0 storage device =>
http://support.microsoft.com/kb/818788/--
For the "allocation unit" decision, it highly depends on what you intend to store on the hdd.
For example, if you are going to store anime (big files in general) go with something like 8KB+
Otherwise with small files, you will waste hdd space. A 25kbyte file will occupy 32kbytes of hdd space if you use an 8KB allocation unit size.