Hi,
after completing mission one I sneaked into there via a hatch, and grabbes a document.
Now, where does this show up, what does it do? Couldn't find it on the clipboard!?

I asked this same question a while ago, it turns out that its just to give the player more back story into the signal ops world

http://www.gog.com/forum/signal_ops/what_is_the_exact_purpose_of_the_secret_archive_missions

It should show up on the clipboard, you might need to scroll through a few pages. it gets removed if you get caught in which case it respawns so you can try again. it also disappears sometime after starting the next mission.

Since the secret document gets removed after completing the next mission, you can never have 2 documents in your clipboard at the same time. This was done so that the player doesn't have to manage the organization of documents. So make sure you read it before completing the next mission, otherwise that information is gone forever! (not really, you can always play an old savegame)