I don't have that many manuals but I have them organized into a ring-bider, sorting them by their set number. You could have multiple binders and divide them in groups.. by theme, by set number range, etc.
As Brickdancer I also just received one of the other 9.999 available... I am definitely going to open it as soon as I go back home. It will be put on display in a frame.. together with all the other exclusive figs.
I know that it will lose £100 just for being opened, but I don't want to stare at a white bag. He'll be fine next to TC-14! Wasn't it a "she"? They'll get along just fine! Unless... :D