When you delete a partition, you delete all the data in that partition.
Didn't say which OS you are installing, but if you are going to cleanly install, say Win-7, and you have all your data backed up, just put the Win-7 DVD in your DVD player, set as 1st boot drive in the BIOS, put in your language, keyboard, etc, and use Custom Install. It willl show you all the partitions on the HDD, and you can just delete them. That leaves your HDD with fresh unallocated space.
Next you can choose how big you want your system partition (always leave some space unallocated for later use or resizing), and Windows will be installed in that partition. It will be formatted with NTFS and labelled C: automatically.
With Win-7 it will also place a 100 MB system reserved partition at the beginning of the drive for the BCD, bitlocker if needed.
When you cleanly install the OS, don't have any other HDD's connected to the MB so all components will be placed in this system partition on Drive 0.
When completed, reattach other HDD's, and reset this Drive 0 to be 1st in the boot order in the BIOS.