I fully second bcmyers's approach. It is indeed perfectly workable, and not only that. It perfectly mirrors David Allen's description of GTD and what is important and less important etc to pay attention to when a person wants to "get organized". You actually do not need much at all. A few sheets of paper. You keep errands on one sheet, agenda items to bring up with your boss on another, "waiting fors" ("people owe me") on yet another, etc. That's pretty much the idea. And then also keep a list (inventory) of projects that will generate new such actions, and possibly a list of AoRs and a few other things. This is all you need. And you can do it all on paper. It is very similar to how millions of people have intuitively handled their todos for centuries, and it is very different from some of the more complex time management and project management methodologies that have sprung up since.
So if you prefer paper or a simple list tool (such as GTasks or Wunderlist) you are all set. You do not need anything more.
But if you want to exploit the power of your computer there actually are things, such as linkages, that you can get almost for free, if you think you have any use for it. For example, linking your actions to projects or your projects to AoRs generally requires no extra clicks. If you are reviewing a particular project and hit the "create new action" button etc, the new action will land in that very project. And if you have associated the whole project with an AoR (either by once having placed it in a "folder" or once having "tagged" it), this association will typically apply to every action that is placed within the project. And there is usually no need to dig into external "project support" files either, because the future actions that you may have identified you have already entered into your app, under the right project, and you keep them hidden there, off your visible next actions lists, until the right time comes.
I guess different people get confused or irritated by different things. Some get confused by all the options and features of computer tools (which sometimes can be astoundingly clunky), and some get more confused by the minimalism of core (paper) GTD (which can appear needlessly ascetic).