You can actually use both methods.  Where possible, I find it easier to expose the CommandBars object from the MainFrame.  I say this because you already have the 'Execute' and 'Update' event handlers established.

If you find that your docking pane is more of a stand-alone item that wouldn't benefit from sharing the CommandBars on the MainFrame, you can create your own instance of CommandBars on that pane.

As a general rule, you can create multiple instances of CommandBars and DockingPane so long as two instances of the same object are not at the same child level of the same container.  If you ever need multiple instances of the CommandBars or DockingPane on the same container, place them in PictureBox controls (for Visual Basic) or Panels (for C#).