Documentation notices

Where do you put the license and notice?

I'd recommend using the standard notice, plus the full text of the GFDL included as a section of the documentation. Then, in each documentation source code, use the tiny license notice (+ copyright notice) that can be found in the FDL Howto.

To make it clearer: the standard copyright and license notices would appear in the resulting printed document, in the copyright page, near the beginning of the book; the GFDL is another section, usually at the end. The tiny notices would not appear in the resulting document, only in each file of the manual source code.

But in the end, every "end-format" (pdf, html) must print out the whole license and one copyright line, right?

Yes.