Ask HN: How do you think about programs?

I've been trying to learn Apple's Cocoa libraries for a few weeks now. I found that writing small applications is a piece of cake, but when I start writing larger apps I tend to get lost in the complexity of my own creation.

My question is this: how do you think about your applications while you're writing code?

Hillegass uses object diagrams (is that what they're called?) to represent relationships between objects in his apps. How do you do it? More importantly, do you use a pen and paper to design your programs up-front (my preferred method) or do you jump right into the code? Do you use diagramming tools to create your object diagrams? Do you write specs? Do you write notes to yourself?

What I'm trying to find out here is an effective method for creating a high level overview of the app I'm working on so that I can tape it to the wall and look at it to figure out what I have to do next. My usual method of writing down TODOs in random notebooks and losing them at college doesn't seem to be working out that well.