chrisKringel - two partitions? are there two partitions? If the phone had a memorycard I would get where you're going.
Let's take a computer for example. When you open up explorer on said computer you see multiple HDD-icons. One for the system, one for Music and Pictures and one for games. This doesn't necessarily mean that this computer has 3 physical HDDs as you can split up a storage device into multiple logical partitions. The computer can easily have only one physical drive.
Same thing goes for our Lumias. They have (as far as I know) only one NAND chip that stores all the data. But this chip is split up into 9 logical partitions, containing the bootloader, serialnumber, mac etc. (head over to the Development Section, a few of the early posts discuss the partitions). When you have a Linux at your hands you can use the DD command to dump every single partition. Of course you should only touch the 9th partition later but better safe than sorry. In order to backup with Linux you have to either run the full dump command from above. When you want to reflash the fulldump every single partitions gets reset to the state from when you created the backup. I never tried this but I would not advise to reflash all partitions. I'd rather advise you to create a single backup of each partition. Charge your phone and enter QUALCOMM mode. Plug it into your Linux and run the commands
Code:
dd if=/dev/sdX1 of=backup1.bin
Code:
dd if=/dev/sdX2 of=backup2.bin
... repeat for every number until the following ...
Code:
dd if=/dev/sdX9 of=backup9.bin
X refers to the mount point where your device is connected. You can use
fdisk -l to get the right letter. When you need to restore your device you need only partition 9, but better safe than sorry

You never know, these additional backups might come in handy sometime...
What do you intend to do? Do you want to have your Apps back after you flashed your phone?