If you install Pro 2.1, it ships with both Jupyter and the ArcGIS API for Python in its default environment -- everything should work out of the box. You can also create environments from the Python backstage (Project > Python), and install packages from that location, without needing the command line. The start menu group for Pro includes a shortcut for Jupyter which you can use directly, or you can invoke it by running "Python Command Prompt", then typing jupyter notebook.
Let me know if that isn't clear, or you need any additional guidance. If you're using Pro, you shouldn't need to have a separate Conda install for the Python API at this time, and Pro 2.1 ships with Python 3.6, so you'll be in alignment on that front.
Cheers,
Shaun