Hi Meikel,
I'm not sure the InDesign+Illustrator is the best choice for your
wireframe documentation.
If you're using a PC, you should take a look at Axure -
http://www.axure.com. I have some friends who have been using it and
they seem very happy with it. I've never used it, as I haven't done
wireframes for a long time, and also because there is still no Mac
version of this software...so, I've never even tried it...But I have
close friends using it and loving it, many of them with an
"Illustrator background".