Q: Where do you put the license and notice?

A: I'd recommend using the standard notice (http://www.gnu.org/licenses/fdl.html#SEC4), plus the GFDL full text included as a section of the documentation. Then, in each documentation source code, use the tiny license notice (+ copyright notice) that can be found at http://www.gnu.org/licenses/fdl-howto.html

To make it clearer: the standard copyright+license notice 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.

ToDo: I wonder how it's done exactly for elisp.texi

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

A: Yes