However you do it, start simple, because you can always get more complicated later. You might have a cool idea in your head -- and then realize that coding it or putting it in the game is harder than expected. That might force you come up with an alternative, so stay flexible with your vision of what the game is going to be like.
In my own experience, I wish I had spent just a little more time plotting things out on paper before writing code, but at the end of the day you really have to just jump in and try things to see what's possible/feasible and what isn't. And the strange thing is, sometimes you have the skills to do something (like create a cool model or animation in Blender) and you still end up having to scrap it because it physically increases the size of your game too much, or causes lag, or conflicts with other parts of the game.