"how to manage these version problems?"
The way that I upgraded from SuSE 8.1 to Fedora is this:
I created a new partition for Fedora. Fedora and SuSE can both use the same swap partition.
I installed Fedora and included the Fedora version of all of my applications and set up SuSE and Fedora as a dual boot system. Once I had Fedora Linux stable then I moved my applications' data one by one from the SuSE partition to the Fedora partition and got each working in turn. When all of my applications were working OK on Fedora I formatted the SuSE partition.
Be prepared. Create a LifeBoat CD.