With the appropriate plugin files residing within inskcape's plugins directory,

-How do I use the extrude plugin? I do notice it adds some new effects.
How to I create ne 3D Polyhedra?

-How do I use the puff feature on a selected Polygon?

Z.

How to I create ne 3D Polyhedra?

You'll need to have a 3D model (in .obj format Blender can create these files) and then place it in the directory of the 3D ployhedron plugin. On my Ubuntu machine that is located at /usr/share/inkscape/extensions/Poly3DObjects

Then, in Filters > Render > 3D Polyhedron type in the name of the file. Use the options in the other tabs to rotate the object and then press Apply to render it in Inkscape.