> But on a general level I'm confused in how to set this software
> up to work with the GTD methodology. From the GTD flowchart we
> have 8 options for each piece of 'stuff'. (Trash, Someday,
> Reference, Next actions, Calender, Waiting, Projects, Project
> Plans) But I'm struggling to know how to set up those 8 things.
For me, OmniFocus is primarily for actions and the elements that give structure to actions. Reference, Calendar, and Project Plans are, to me, not actions, so to me they don't really belong in OmniFocus.
That said, to address your eight items:
Trash: No need for a place for this, IMO; I just delete the item.
Someday: I have a folder for "Someday Projects", and a single-action list for "Someday Project Seeds". Someday Project Seeds are items that would be projects if I worked them, but I'm not interested in setting up the project structure until I'm closer to ready to work the project. Someday Projects are usually projects that I've started working on, but they're on indefinite hold because something out prioritized them.
Someday projects are set to On Hold; the project seeds, which are entered as actions, have a Context of Info, which is On Hold. It might make more sense to have another On Hold context _named_ either On Hold or Someday, but I like all items that are indefinitely non-actionable to have the Info Context.
Reference: I do have a folder called Reference. Everything in it gets my Info context. However, this folder definitely doesn't hold _everything_ that qualifies as reference, it mostly just stores miscellaneous factlets that don't rate a folder in a filing system. If I had another satisfactory place to store these factlets, they wouldn't be in OmniFocus.
Reference also holds a variety of lists - Things to Read, Things to Watch, Things to Learn, Recipes to Try, Stuff to Buy, stuff like that. I'm not sure if these are technically Reference, Someday/Maybe, or Project Support Materials, but I like them in Reference so that's where they go.
Next Actions: Actions show up in various OmniFocus Perspectives, which are usually in the Context side of the application. JJW provided an example. Remember that when you've done all those settings, you can save them and you're done - you never have to define that perspective again.
Calendar: I don't feel that OmniFocus is the place for my Calendar. Nevertheless, I do have a single-action list for "Calendar Events", just so they'll pop up when I'm looking at my list. I consider this cheating, but I do it anyway. I do also have actions related to Calendar events, like, "Gather problem reports for Friday meeting". I don't consider this cheating.
Waiting: An Action may have a Context of Waiting. But I don't put it in a Waiting folder; it stays in its project. Does GTD really want Waiting to be in an entirely separate folder, rather than keeping actions that are Waiting with their project? That isn't how I remember the system, but I could be wrong. If I do want to see all Waiting items at the same time, I go to Contexts and look at that Context.
Projects: Projects are explicitly supported.
Project Plans: Project plans don't live in OmniFocus. Oh, sometimes I have a single-action list called, let's say, "Widget Project Agenda" where I keep random thoughts about the Widget Project. But a project plan of any complexity or formality doesn't, IMO, belong in OmniFocus; that, like calendars, is not what OmniFocus is for.
Gardener