One thing that bothers me about the Wiki is the odd "separation" between the Manual and the "Using" documentation. Isn't it really "all" the manual? So, what do you mean by "manual"? I think that if you're going to re-organize it, then re-organize the manual section and really break it out so the whole wiki is your manual.
Heck, it'll make future iterations of your Help File easier to make. Just dump the contents of the wiki, clean it up, and Help-ify it.
I don't know about the completely separate Audio, Video, and Images "sections". I'd put them "under" the View Schemes section. I've already made a good start on View Schemes in the Wiki (though I lost steam there... I do intend to get back and finish that page sometime soon).
And I'd bust out a Full Section on the different Views of MC (ie Theater, Display, Standard). So something more like this:
1. Installation
1a. Installation Options
1b. Licensing and Purchase
1c. Trial notes (something about how the 30-days is once per major version of MC, even if you don't use the product in that timeframe)
2. Getting Started
2a. Importing
2b. Playback (Concept of Playing Now and basic description of how to Play stuff.)
2c. Basic Application UI control scheme (explain the control "motifs" -- how the divider bars work, right click on things, drag-and-drop, etc. Teach them how to find the stuff they want and how to work the "buttons", if you will.) Explain the Tree conceptually and how it relates to how to navigate around the UI (leave alternative navigational methods for the more advanced "view modes" discussion below). Pointers to more advanced later discussion of View Schemes and Options.
2d. Very basic description of the regular Views (display, theater, standard, mini) and how to switch between them. Pointers to more advanced later discussion (in this section, don't worry about trying to explain all the options, just show it how it is by default).
2e. Basic concepts of "tags" and "tagging" and how this relates to the views of your media MC shows.
3. View Schemes
3a. What are View Schemes? How are they organized? How do they relate to what media you see and to filters?
3b. Basics of how it is by default.
3b1. Audio
3b2. Video
3b3. Images
3b4. Documents
3b5. Playlists and Smartlists
3c. Customizing View Schemes and Creating your Own.
3d. Advanced Uses of View Schemes (filtering on Playlists, Advanced Expressions, and other fancy-pants stuff that we come up with).
4. MC View Modes (include full discussions of navigational methods, different "views", split views, tabs, Theater View modes, how the different modes relate to one another, etc)
4a. Standard
4b. Theater
4c. Display
4e. Mini
5. Not sure what to call this section, but I'd say there should be another section that covers this stuff sort-of "together". Devices, Services, and Plugins or something like that.
5a. Podcasts
5b. Devices (including Handhelds, TV tuner, Ripping, and Burning)
5c. Services and Plugins
5d. Remote Control
5e. Image and Audio Editor
5f. Importing from Cameras and Camera Cards.
6. DirectShow and Audio Playback Concepts (high-level "this is how it is" stuff)
6a. File Format Support. Discussion of Media Types (documents vs video vs images vs audio)
6b. DS Playback Guide (of course)
6b. DVD Playback stuff
6c. Audio Formats and settings used for ripping. Difference between Lossy and Lossless. Transcoding concepts, etc.
6e. Image details. Raw images, editing, rotating, etc.
6f. I'm sure more will come up here.
7. Tagging. Explain the concept of the database and the concept of "tags" and how MC uses them for everything, in detail. How to do it in all the different fancy ways.
8. Options. Every option -- rip the content on options from the manual. Put it all in one place, systematically, and then when links need to be made from other relevant subsections, you can easily just link to the relevant option in this section.
9. Zones and Advanced View Uses *
9a. General Overview of Zones concept.
9b. Configuring Zones (what options are zone-specific, how-to type stuff, etc)
9c. Detached Displays, multiple displays, and other fancy setups.
* Special Thanks to fitbrit for suggesting the Zones section.
10. DevZone
11. Troubleshooting. Hardware discussions. FAQs on Anti-Virus and solutions, etc.
12. Support