Need some more clarification:
1. Is the 1 TB HD (I assume that is what you meant when you typed "1gb.HD", as that little space would not support a partition for El Capitan and your other "stuff", the small 969MB partition, and the one for Bootcamp) internal, or external?
2. If it is internal, do you have a backup to an external device? That is so, so critical!
3. To make sure the drive is OK before you Erase and Format it, launch Disk Utility, select the drive itself (not any of the partitions), and click on First Aid, Hoepfully, taht will not reveal any serious issues.
4. To Erase and Format the complete drive, you would need to launch Disk Utility (externally, if the drive is your internal one), select the drive itself (not any of the partitions), then click on Erase, and make the Format "Mac OS Extended (Journaled)", and the Scheme "GUID Partition Map". Next, click on "Security Options", and on the screen that appears, move the slider to somewhere near the middle. It will then Erase and Format the drive, although it will take some time.