When you clone a drive, it copies sector by sector everything on that drive to another drive. It doesn't make any difference if you have 1 or several partitions on the drive, it will clone everything over to the new drive and overwrite everything on the target drive. Some data transfer programs will proportion the partition sizes to match the size of the target drive. But you can't clone just a partition, it clones the physical drive.
You can image a partition of one drive to another for storage or backUp, like the Win-7 builtIn imaging applet does automatically.
Or you can BackUp Files, or Folders, or a whole drive to another, either uncompressed or compressed.
One good source to understand the differences is to download the Acronic True Image 2011 Manual to read or review
Here is the link to download it.http://www.acronis.com/support/documentation/index.html
Hope that's helpful