If you do not want to create your theme's design outline on paper, then there are tools available to help your create and visualize theme designs. One particular package called Balsamiq Mockups seems to be at the forefront of this technology, and I am reliably informed that Moodle.org uses this software package to help visualize designs and the flow of information through Moodle applications.
The following figure depicts a Balsamiq web application:
Here is a figure of our wireframe made by using Balsamiq Mockups but in more detail. As you can see, it's very easy to conceptualize the design and even the general Moodle functionality by using such software.
This software is not free and is priced at $79. So if you are creating only one theme for Moodle, it might be a cost too far. However, at $79, it's not a huge expense for a commercial organization. You can try it for free by using the web-based version. Go and have a look; I think you will find it rather...