Ahoy!
After reading that many users of SSE have been left without a user manual in their boxed version.
Or if you can not find it with the download version.
Don't worry!
You can find an online version of the manual below:
http://cdn.steampowered.com/Manuals/48800/PDX5605US_ShipSimulator_OnlineManual.pdf?t=1282991603
It may appear that the download is taking ages, but give it atleast 3 minutes even on the white screen.
It's a large manual, but trust me it is downloading still!
I hope it can help you out, and if you stil wish to have the manual on paper.
Then please contact VSTEP or Paradox
Kind Regards
Matthew