I suppose with the onboard-perl from my linux-distribution I don’t have to care about updates. What is the right way of doing updates when I have build my perl from sourcefiles?
Your first sentence seems to be contradicted by the second. Do you maintain your Perl via your linux distribution's package manager, or do you build it from source?
If you build from source, simply download the new distribution, build it and install it like you did the first time. It will overwrite old versions of executables and libraries with new ones as needed, but won't delete anything you have installed via CPAN.
There's no trick to it really.
You need to re-build from source. Since you can run any number of parallel builds (just install it in a different directory, and point your code to it in the header), this actually offers a few advantages over using a package manager. You don't have to update code if you don't want to, you don't break compatibility when you want to try out something new.
The one thing you really need to NOT do is mix package manager and building from source. Pick one, and stick with it. If you don't you're going to have significant issues.