|As the others have said, the hidden partition is probably the recovery partition which means you are most likely asking about an OEM system (Dell, HP/Compaq, Gateway, etc).|
I can tell you what I did when I bought an HP laptop in the fall. I created the full set of recovery discs (7 DVDs), then deleted both the Recovery & HP_Tools partitions. That left me with the hidden System partition & C: partition, plus unallocated space. I combined the unallocated space with C:, then divided C: into 2 partitions (one for Windows & programs, the other for storage). In the end, the 500GB HDD was partitioned as:
System (hidden) - 200MB
C: (OS) - 200GB
D: (Storage) - 265GB
I did all the above using EASEUS Partition Master Home Edition.