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Unless I'm overlooking something, the tool palette is a little strip of about 8 buttons, each for a different Graffle tool (shape, pen, line, text, magifying glass, etc.). There is only one Graffle tool palette, but you can customize which tools are in it.

A stencil is a collection of common shapes, to save people the time of re-creating them. Graffle has several stencils pre-installed, like Basic (square, triangle, circle, etc.), or Office Layout, (desks, couches, bookshelves, etc. for laying out a floorplan). You can find more stencils at www.graffletopia.com, or even create your own (check the Stencils menu).