Content distribution among top navigation menu and home page

[arkana]

We are in the doc site planning stage and would like to know how to layout different content in the top menu (we are using HTML5 top nav template) and the home page, and how to set up the TOCs accordingly. We want to cover all content types (online help, user guide, release notes, etc.) on the home page and the menu, but would like to distribute them logically, evenly, and naturally so that it won't duplicate everything in both places. So we will put user guide in the menu and put the entry points to online help on the home page, for example. For items whose entry point are from the home page, we still want to use the side menu (generated by menu proxy) as those topics accessed from the top menu. For content that should appear in the top menu, we just organize them in the master TOC and associate it with the target; For rest of the content, we organize them in separate TOCs, but not sure how to associate these TOCs with the Home page items. If a icon on the home page opens the entry topic for the online help of one of our products, will the side menu display the TOC that includes that entry topic? How Flare's target know about the TOC if we are not linking it with the master TOC? How to set up the Flare project to achieve my goal here?

Thanks