James, if you look down in this forum a bit, you'll see my "manual disappointment" post where I say much the same things as you do here. I think the html manual is fully what would have been printed up, so nothing was lost. In that thread, Malfador and Shrapnel state there was too much detail for them to broadly cover all possible questions in the manual, but they are going to put up a web page which answers specific detail questions.
In the meantime, your best bet is to read the forums here (and I also like the SE4 Center ones at:
http://www.connected.bc.ca/~thomas/se4/ )
There's a lot of very knowledgeable people on the forums and you can pick up a lot if you got back a few pages and read the old Posts. That's how I found out a lot of stuff.