Going over the technical differences of conda and pip:
So Conda is a packaging tool and installer that aims to do more than what pip does; handle library dependencies outside of the Python packages as well as the Python packages themselves. Both have many similar functionalities as well, you can install packages or create virtual environments with both.
It is generally advisable to generally have both conda and pip installed since there are some packages which might not be available with conda but with pip and vice versa.
The commands to install in both the ways is easy enough, but one thing to keep in mind is that

conda stores packages in the anaconda/pkgs directory
pip stores it in directory under /usr/local/bin/ for a Unix-based system, or \Program Files\ for Windows

You can use both pip or conda inside the jupyter notebook, it will work just fine, but it may be possible that you get multiple versions of the same package.
Most of the times, you will use cmd only to install a module used in your code, or to create environments, py -m pip install "SomeProject" here basically means that the module "SomeProject" will be downloaded in base env.
I've been coding with R for quite a while but I want to start learning and using python more for its machine learning applications. However, I'm quite confused as to how to properly install packages and set up the whole working environment. Unlike R where I suppose most people just use RStudio and directly install packages with install.packages(), there seems to be a variety of ways this can be done in python, including pip install conda install and there is also the issue of doing it in the command prompt or one of the IDEs. I've downloaded python 3.8.5 and anaconda3 and some of my most burning questions right now are:

When to use which command for installing packages? (and also should I always do it in the command prompt aka cmd on windows instead of inside jupyter notebook)
How to navigate the cmd syntax/coding (for example the python documentation for installing packages has this piece of code: py -m pip install "SomeProject" but I am completely unfamiliar with this syntax and how to use it - so in the long run do I also have to learn what goes on in the command prompt or does most of the operations occur in the IDE and I mostly don't have to touch the cmd?)
How to set up a working directory of sorts (like setwd() in R) such that my .ipynb files can be saved to other directories or even better if I can just directly start my IDE from another file destination?

I've tried looking at some online resources but they mostly deal with coding basics and the python language instead of these technical aspects of the set up, so I would greatly appreciate some advice on how to navigate and set up the python working environment in general. Thanks a lot!
Installing packages in python and setting up the working environment