I've used Acronis Disk director suite and partition magic many times and both create a small partition like this, for partition data. I've deleted and reformatted many different types of hard drive and in every case I deleted the smaller partition first, leaving only unformatted space.
As long as you partition and format correctly prior to installation it doesn't really matter, though to be safe I'd always use any drive formatting software that the manufacturer has available such as Maxblast, for maxtor drives.
I also believe that the MBR or memory boot record is held on such a partition though Im not entirely sure as I use a boot manager from Acronis myself, which i think resides on the first sector of the primary partition - i.e the larger one.