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What are the External Libraries in a PyCharm project?

I'm a bit confused on this and can't find a satisfactory answer searching elsewhere - everything is about using external libraries in some way or another.
In my PyCharm projects, I've got your project root directory, which contains a venv. This venv of course contains the python executable relative to the project, as well as the relevant site-packages and modules I've downloaded via pip or whatever.
But there's always an External Libraries section, that has it's own Python executable, venv, .gitignore, site-packages, etc.
Is this normal? What's the purpose of having two venvs in the same project?
Thanks!

You only have one venv normally in your Project
The other Python Executable should be the global one.
Normally you use a venv to keep track of the needed Packages for this specific project. So that you don't confuse other Packages with other projects or have dependency/Version Issues
If you want you can also use the global Installation of Python which would not create a venv

Can I Store Extra Info In My Python venv?

What I want to do is store a reference to the project location (my source files) in my venv.
The purpose for this is so I can automatically switch to that directory when I activate my venv.
I already have a script that managers my venvs. e.g. workonvenv xyz will activate the venv named xyz.

Why not add this logic to the script that manages the venvs?
A venv is not tightly coupled with a project, meaning venvs can be used for several projects and a project doesn't necessarily need a venv to work. Therefore there's no reference of a project in the venv.
What I recommend is to define a convention for project and venv names such as - project: "project-x" and venv: "project-x-venv" and then use your script to activate the venv and then cd into the project folder according to this convention.

Where can you use packages installed in python virtual env?

I'm a huge beginner so I'm not very informed about how packages really work. I know that you should create a virtualenv in your project folder to avoid version conflicts etc, and you're not supposed to put your actual project files in the virtual env. So if your project files are in your project directory on the same level as the virtualenv, can your project files "access" the things installed in the virtualenv? Can files outside of your directory access packages in your virtual env?

Yes, it all depends on the context. Your virtualenv can exist anywhere, be it in your project directory, or somewhere else.
When you want to use the virtualenv, you just have to call source command on it. Then whatever python command you execute on whichever file, will have access to the virtualenv. For example, if you store your virtualenv in /home/user/project/virtualenv, then you would do
source /home/user/project/virtualenv/bin/activate
Then whatever you with the python, it would be the version installed in virtualenv.
You can double check if you're using the global python or the virtualenv python by doing which python. It will either point to the global python path which is usually under /usr/bin/python or /home/user/project/virtualenv/bin/python.
So normally, you first do the source command, then you can do pip install on whatever packages you need already. It will be installed in the virtualenv and it will not conflict with other projects.

Changing Python Packages Path for Django Application

I'm currently hosting with a dreamhost shared VPS. I do not have sudo rights. I want to install django packages but I cannot to /usr/local/lib/python2.7/dist-packages/ because python is root access only. I have setup a directory in my user directory also called dist-packages to which I have copied all my packages to. I want to use the packages in the dist-packages directory I created to build my django app. Is possible to use my packages? I'm looking for a work around. I do have virtual python env installed, is there a way to use it maybe?
Python 2.7
Django 1.9
My current setup
/home/myuser/mydomain.com/
env/
myApp/
passenger_wsgi.py
public/
How do I setup the env?

You should be using virtualenv for sure(I'm surprised that you are still looking for a work around). It's really inconvenient to use default python for everything. virtualenv will create an isolated python directory of your choice and install everything in there. When you want to use it, just "activate" it then you are automagically in that python environment.
It's almost trivial to learn how to create one, you can even create as many as you like, each with different packages installed. Check their doc for more details.

Virtualenv, Django and PyCharm. File structure

I am newbie using VirtualEnv and recently try to create one using PyCharm. During the process, PyCharm ask me to specify the project location, application name and VirtualEnv name and location. My doubt is, after I specify the name and location of the VirtualEnv the location of the Django project files must be inside the VirtualEnv? or it's possible to have the VirtualEnv files in a different location than the Django project files?
Maybe I am not understanding the purpose of the VirtualEnv. Perhaps, VirtualEnv it's just a list of the dependencies of my project, Python version, Django version, Pip version, Jinja2 version and all other required files, but not necessarily the Django application files (the website that is being developed).
Thanks in advance.

Ya, I think you misunderstand what virtualenv does:
https://virtualenv.pypa.io/en/latest/
The basic problem being addressed is one of dependencies and versions, and indirectly permissions. Imagine you have an application that needs version 1 of LibFoo, but another application requires version 2. How can you use both these applications? If you install everything into /usr/lib/python2.7/site-packages (or whatever your platform’s standard location is), it’s easy to end up in a situation where you unintentionally upgrade an application that shouldn’t be upgraded.
Your project files don't need to be (and shouldn't be) where the virtualenv files are.
virtualenv installs your app's python dependancies in a folder for the specific virtualenv that is being used.
Let's say you are not using virtualenv, the dependencies would be installed into into the site-packages folder for your system. The dependancies aren't installed in your project directory and your project directory isn't in your system's site-packages directory.
Using virtualenv doesn't change that, it just changes where the dependencies are installed.

virtualenv is not just a list of dependencies! It actually has all the modules under its umbrella. Think of a virtualenv as a space which isolates all the packages used by your project from the rest of the other packages that were installed previously or at a later time.Yes, there is an option to have the virtualenv make use of packages that are "outside" of the environment but that's just an option.
The main purpose of having an virtualenv is to enable the user to use packages versions of his choice and keep them isolated from the rest of the space. Usually, the list of packages belonging to a specific virtualenv are captured into a file, requirements.txt. If you want to run the project on a different machine or share it with someone, having requirements.txt will make it easy to recreate the environment via pip install -r requirement.txt from within virtualenv