Template decisions

I am quite dissatisfied with my web site template. I tried to pick the best one, but they all are horrible enough to my taste. The main template issue is categories. I need to think about some nice way to organize them, so that they will be easily viewable.
What I thought about is something like that:
1. Make subtopics in every category. This is, Calculus, Linear Algebra, Number Theory, Topology and so on in math and Mechanics, Cosmology, Electricity, Quantum Physics etc in physics.
2. Organize the links in two columns instead of just one.

I hope I will manage to finish this by the end of the week.