Clonezilla is useful for that task related to "cloning" (tested by me). The "Install" Procedure should be better if you run it from the installation disk and start from scratch.
With Clonezilla, you can clone your USB's system into a hard disk drive, after which you will have a hard disk drive with the partitions as in your USB with extra unused disk space. (It would be cool if you provide us with the current partitioning sizes of your USB in order to give you a more comprehensive scenery).
You may wish to use all the hard disk drive capacity for the system. If so, you will simply need to start again from your USB, (the current one you use for booting or a live CD), then use gParted, erase your current swap file system in order to preserve your boot partition in one piece, and write a new swap at the very end of the partitions.
The procedure itself will delay a while depending on your hard disk drive capacity but it is easy indeed.
This procedure is how I cloned my 4GB USB system into a 8GB SD Card and some other cases with hard disk drive.
If you need further details please provide a screenshot of your current partitions in gparted, let us know how much memory does your computer have and the size of the hard disk drive where you wish to clone your system.
Cloning your system will preserve all your software, documents, configurations, etc.