When you set up a drive with 2 partitions, what you actually create is one primary partition, an extended partition & a logical partition. The logical is created inside the extended.
It sounds like what may have happened to the second drive, is that the logical partition didn't fill all the space in the extended partition. This would leave you with 2 accessible partitions & an area of unallocated space which can't be formatted due to it not being partitioned.
The advantages of having more than one partition on a storage drive such as yours, are :
1. partitioning allows you to designate different partitions for different purposes. eg one for downloads, one for CD burning, one for important documents or backup etc. This has the obvious advantage of making your files easier to locate.
2. defragging is faster
3. If you share files over a network, you can restrict access by only allowing sharing on one partition.