You can use manual partitioning in the installer to explicitly set what partition to use as your root, and which one as your home – and which one is your EFI when applicable.
Just be careful not to format your home partition in order to keep its content!
Regarding KDE, Manjaro using (presumably) a later version, the configuration should update itself on the first run. You can make a backup of the configuration folder beforehand, just in case.