Using a bit of topic-necromancy here 'cause this post just made me realize I could actually have a good way to do the help in a non-immersion breaking way.
The game I'm currently working on is a retro-sic-fi setting (think tech levels live Alien), and one of the dropables I intend to have are magazines (I'll explian that when I eventually reach the end of the design section of the forum and write down a post explaining my ID-subgame).
So one idea to have a in-game manual is to have a item, with a 100% chance to drop on the first room or already in the player inventory, that is a game manual.
"you find a old computer-game manual in the floor. (R)ead? (D)iscard?"
Upon reading it would be a normal manual (sections etc).
Another thing I might do is use the consoles I'll have spread around the levels (requiring that the player begins the game logged on to a terminal, which would make sense with plot/gameplay mechanics) and have a "type man and press enter to read the manual", but this seems to be more immersion breaking, since that manual would have to explain keys and etc.
I'll keep thinking about this, but thanks for the ideas!