Sounds good using both backups for security, but doesn't using iCloud backup affect iTunes backup or visa-verse.?
No. The backups are separate.
Here is the main differences.
iTunes restores your iPad to factory, restores the data and settings, and then re-syncs your apps and music from your iTunes library. It will normally do this automatically, but sometimes you have to initiate the sync. As long as it is done immediately, it works. If you delay then you have to start over again, because when restored data has no app to belong to, eventually it goes away again.
The first two steps are the same for iCloud, but instead of re-syncing from your iTunes Library the apps and other iTunes content are downloaded from the iTunes store. This part can take a long time, depending on your network connection and number of apps. After the initial restore your iPad is usable, but the apps will be ghosts until they finish downloading. If you have lots of apps It is sometimes necessary to restart the iPad a few times, to kick the download process in the rear when it pauses.
I may have the fine details wrong, since I'm typing from memory.
Anyway, that's my experience.
Here are some Apple support pages on the subject:
iTunes Backups
http://support.apple.com/en-us/HT4946
iCloud Backups
http://support.apple.com/kb/PH12519