Packages from OS or from custom package manager

I would choose the package provided by your distribution/operating system.

Because if you do that, then your package-manager will know that these libraries are installed. (They usually don't check if the libraries exist only if the package with the libraries is installed.)

And if you try to install another package which depends on those libraries, you either

• have to tell you package manager somehow that the libraries are already installed (for example by creating a pseudopackage for them)

or

• the package manager will install the packages with the libraries and you will have two versions of those libraries on your system.