Hi Korvo,
Although lots of research has already been done, the research is not complete yet. However, I did learn some things that might help you get started...
First of all, medical marijuana has been used to treat such diverse conditions as "nausea (especially as a result of chemotherapy), loss of appetite, chronic pain, anxiety, arthritis, cancer, AIDS, glaucoma, multiple sclerosis, insomnia, ADHD, epilepsy, inflammation, migraines and Crohn's disease."
Marijuana works because it contains cannabinoids similar to endocannabinoids produced naturally in the human body, where they mediate a variety of responses. The receptors for these natural endocannabinoids are found throughout the body, but are especially prominent in the brain, as you can see in the graphic below.
So I think the answer to your question would be that where medical marijuana works depends on the condition it is used to treat!
And then here is the link where I found this information: http://science.howstuffworks.com/medical-marijuana1.htm