I would probably use Isometric Grid Paper (Score 2, Informative)

Here's one resource, Constructing Isometric Grid Paper, A Computer Aid, but you can buy it at places that sell engineering drawing type supplies. Or at least you used to be able to. I would start at the bottom in the middle and darken in the edges to show which blocks are to be filled in. One problem with this is that you are kind of limited in complexity. If it's too complicated it will be tough to tell what is going on. Even if its pretty simple there are still going to be points at which clues overlap, and that is going to make it hard to understand. I like the idea that someone else had of using hex paper, I think that would be easier to do.