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Aubrey:
What you intend to do is not really very practical, for several reasons. First, the main menu is dynamic: when you click on some modules, they open to show suboptions. Also, when you add a new module, its link appears automatically in the main menu (if you've set its weight to a value different from zero).
So, if you really want to have some (not all) of the menu options up there, in the header, you need to sacrifice some of the flexibility of the default menu.
Let's assume you absolutely need to place some options there. You can begin by exploring the x2t theme that comes included in your XOOPS distribution. This theme has a row of menu options on top. You can replicate this functionality for whatever options you want. Just check the way the links are built.
Another option is to go for a horizontal hierarchical menu, an option we're exploring for the upcoming opening of the XOOPS Net sites. This would sacrifice some functionality, but would give you more space and a different look.
Whatever you decide, don't be afraid to play with options, even if you think them "clunky". In the XOOPS world, playful exploration IS the way to go.
Cheers.