if you want to backup you could as others have suggested boot from a liveCD and rsync the files or do a dump of the unmounted filesystem.
If you are uncomfortable doing this, you could look into using some 3rd party products to help you. Mondorescue is a pretty cool utility that will basically create an ISO image of your HD, similar to Norton Ghost. Benefit of this is that using Mindi to restore this, you can either choose for the restore to basically format the destination HD just like the original, or you can do a selective filesystem restore. - Or, you can choose to do a directory level restore all from the same backup.
Its pretty neat, NASA were using it at one time, not sure if they still do, but its free!!
It might be a bit more help to the guys trying to help you, if you can provide a step by step list of how you config'd your system, as giving advice on redoing a partition scheme when you dont have all the facts can be a bit daunting :-)
hope that helps.