Omnifocus can, admittedly, be daunting at first. I recommend doing what David Allen refers to as a mind sweep - get all the ideas, projects and actions out of your mind and onto a page. I see two major ways to do this; either go straight into Omnifocus, or start somewhere else and then transfer over a list of projects and actions.
Whenever I've rebooted my system, I just get started. I've done this a few times when I realized that I'd fallen far behind, or had been trying a different task manager, but I always end up coming back to Omnifocus. The advantage to going straight to Omnifocus is that it feels like you're really getting started. As you notice logical groupings, you can make those intro projects or actions with sub-actions. I'll write more on both of those later - usually I use high level projects but many of my actions have sub-actions, so David Allen would call them projects. The reason for that is that is that many of my projects are open ended, such as maintain this blog, but I'll have chained events like research Facebook's new app paper, get pictures of paper, write review etc. I'll make each of those a sub action under review paper, in the Omnifocus project "Write TedMartin.Me". I use a few folders for the highest level groupings like Home or Work or Blogging. Each of those folders has its own single action lists.
Once you have a list of projects, actions and sub-actions, think about what you'd need to do them. I'll write about contexts in the next post in this series, but start with physical constraints - what can you only do at home or at the office. I also use energy and time levels - dashes, focused work, reading and reviewing and low-energy.
Finally, after you have a rough sort of actions and contexts, take a look at your actions and make sure you've written them with an action verb: write report on staff member or email tom about lunch rather then make lunch plans.
The other option is to do your brain dump somewhere else, like Word or on paper. Than Pham at Asian Efficiency appears to use excel when you look at the screen shots, first listing tasks, then doing a rough high level sort into categories like Work or Home, and then by projects and lists. The advantage to doing this in excel would be that you could see it all in one place and then do filters and sorts as you add each level in the hierarchy. I prefer to build out my hierarchy in OF from the start, but I think this could be a great approach if you have a lot to get under control.