3d models are not really managed. The footprint points to the files directly.
But you can use environment variables.
I am not sure what you mean with using relative paths. If i remember correctly entering relative paths into footprint settings will mean it is relative to the KISYS3DMOD path variable.
A detailed explanation is found in Tutorial: How to make a footprint in KiCad 5.1.x (From scratch)?
And this can also help: Library management in KiCad version 5