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The three-point alignment method produces exact tracker/vertex matches for a small number of points. Alternatively, you can use the Align Via Links dialog (launched from the Linking submenu) to align a mesh as best possible to any number of links.
You should establish all your links first, using the Add Links to selected menu item. Then launch the dialog.
You can align the mesh to the trackers, or cause the camera and all the trackers to be moved to match the mesh, leaving it right where it is! This second option is useful when you have been given an entire existing 3-D model of the set that you must match the solve to.
On the dialog, you'll notice that you can control whether or not the mesh is allowed to scale to match the links, and whether or not that scaling is separate on each axis, or uniform. When you have a complex existing mesh to match, you'll certainly want uniform scaling. But if you are matching a box to some trackers, and do not know the correct relative sizes of the axes, you should use the non-uniform scaling.
You can also cause the tracker locations to be locked to the mesh locations, which is handy when you have aligned the world to the mesh position—the created links will cause the solve to reproduce this same alignment with the mesh later, in additional solves, without having to re-run this dialog.
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