Use a specific python.exe instance with PyMOL/Windows?
So it is really hard to make a given python instance run a library from a different instance. It is not just one dist-packages library folder, but multiple that you would need to link, and all that assuming they use the same version of python.
So the best bet is to install a new instance of pymol the python module.

The module can be installed in a python that uses conda with

conda install -c schrodinger pymol


This is the incentive version of PyMOL 2 and does not require a licence.
You installed rdkit, so I am assuming you used conda as conda install -c rdkit rdkit. But just in case you went through the pain of compiling rdkit for a given python instance without conda and want the same for PyMOL. There are guides of instructions required to compile open source. Such as https://pymolwiki.org/index.php/Windows_Install. On a barebone OS like a Pi's Raspsian, I had to do a lot more than claimed say sudo apt-get install python3-dev libglm-dev freeglut3-dev libglew-dev libpng12-dev libfreetype6-dev build-essential libxml++3.6-dev and link a few things manually. So just like for rdkit, conda make life a breeze.

PS. RDKit and PyMOL? Add PyRosetta and you just my favourite modules!