Knowing where you are located would help folks be best able to give you the most specific advice. If you click into the soil/mulch forum, do some reading, you should find a lot of useful info.

"When I cut the tree stumps to the ground do I have to remove them before I can deck on top? Will they grow back? Is there a organic/natural way to kill the root?"
This depends on what it is. ID'ing any plants in question on the name-that-plant forum would be a good start to answering these questions.

After I have cut all the grass and other plants do I also have to treat this area before decking it, to stop unwanted growth underneath or is the lack of sunlight sufficient?"
This will eliminate grass, and *likely* anything growing in full sun, but some tough characters could just creep along under there until finding a way out into the sun again. If there are any plants besides grass in question, finding their ID would be the first step to answering this question.

"In your opinion which is the best wood for building raised beds?"
Treated lumber and organic gardening don't mesh, which I mention because you asked about an organic way to kill stumps. Untreated lumber can rot very quickly. Not sure of your degree of organic concern? Any options besides wood?

"I want my raised beds to be around hip height but this will be a huge amount of soil to fill them up, can I fill the bottom of them with rocks or gravel and should there be a layer of something between the raised bed and the ground underneath?"
Knowing where you are/your climate would be necessary to answer this question accurately for your particular situation/location. And what you intend to grow.

"As I will have a mammoth amount of plant waste from clearing the garden(the weeds now come up to my shoulder) I would like to put it to good use, can I compost it and then use it for the raised beds or will I then get weeds in the beds?"
If there are seeds, they may sprout. Some roots/stems are able to keep growing until 'all the way dead.' You may need to stir things up a bit if you see stuff in an open pile trying to keep growing.

"Do I need to put anything in with it or will it just be fine if I leave it alone in a big pile?"
It will decompose no matter what you do, more quickly in a pile. I would probably generally use this material as the base layer for the raised beds, without composting it first, though know it will shrink as it decomposes. That's fine if you are making more compost as mentioned, you'll top-off the beds with it periodically, which is a good thing.