Confused about DBus
So does this mean that my website needs to run a DBUS service to
allow me to call methods from it into my program?

A dbus background process (a daemon) would run on your web server, yes.
In fact dbus provides two daemons. One is a system daemon which permits
objects to receive system information (e.g. printer availability for exampple)
and the second is a general user application to application IPC daemon. It is the
second daemon that you definitely use for different applications to communicate.

I am coding in Python, so I am not sure if I can run a Python script
on my website that would allow me to run a DBUS service.

There is no problem using python; dbus has bindings for many languages (e.g Java, perl, ruby, c++, Python).  dbus objects can be mapped to python objects.

the most logical solution would be to run a single DBUS service that
somehow imports method from different programs and can be queried by
others who want to run those methods. Is that possible?

Correct - dbus provides a mechanism by which a client process will create dbus object or objects which allow that process to other services to other dbus-aware processes.
Ok, so, I might be missing the plot a bit here, but would really like some help. I am quite new to development etc. and have now come to a point where I need to implement DBus (or some other inter-program communication). I am finding the concept a bit hard to understand though.
My implementation will be to use an HTML website to change certain variables to be used in another program, thus allowing for the program to be dynamically changed in its working. I am doing this on a raspberry PI using Raspbian. I am running a webserver to host my website, and this is where the confusion comes in.
As far as I understand, DBus runs a service which allows you to call methods from a program in another program. So does this mean that my website needs to run a DBUS service to allow me to call methods from it into my program? To complicate things a bit more, I am coding in Python, so I am not sure if I can run a Python script on my website that would allow me to run a DBUS service. Would it be better to use JavaScript?
For me, the most logical solution would be to run a single DBUS service that somehow imports method from different programs and can be queried by others who want to run those methods. Is that possible?
Help would be appreciated!
Thank you in advance!