Changing Linux partitions is quite safe. How you do it depends on what distribution you're using. I have used HardDrake in Mandrake 9.1 to re-size Windows FAT32 partitions, converted FAT32 partitions to Linux reiserfs partitions, and have re-sized Linux partitions (reiserfs again). It is a very capable tool that it easy to use provided you take your time and think about what you are doing. I don't know about qtparted, but if it came with your distribution, then it's probably safe to use as well.
As with all fundamental operations you perform on your storage devices, it's important to backup all your data (both Linux and Windows, if applicable) before you change any partitions.
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