I`m not totally certain about Paragon but for Acronis when you clone a drive, the PC will reboot on completion and use the `new` drive. The `old` drive needs to be reset as it contains exactly the same as the new copy and you can`t have two C: drives. Also worth mentioning is that cloning is generally used when replacing a HDD.
For backup purposes an image is produced which should be kept on a separate drive (not partition) or external HDD. This can generally be `updated` with `incremental` or `differential` backups although it takes very little difference in time to create a new archive. Using this method of `backup` rather than `cloning` is less time consuming and doesn`t require opening the PC each time.
The only other method open to you would be to use RAID click here but it reduces the space available and doesn`t sound as if it`s what you`re trying to achieve.