It depends on what file system you are using on your HDD's partition. You could be wasting space if you are not using NTFS. If you are using FAT32 in a 32k cluster, then you could be wasting space. (I'm assuming that your OS is W2k/XP) You may have to get a program called, "Partition Magic" to change your file system and reclaim wasted space.
Here some old information in a PDF format on <A HREF="http://www.wdc.com/library/legacy/EIDE/fatfile.pdf" target="_new">FAT File System</A> in the simplest form, but very clear. Also, here is some info I posted in a later thread regarding cluster sizes. Hope this helps with your question.