First of all, welcome to Subsim.
In SH3Commander, click the ? at the far left of the interface for the user guide, should answer most of your SH3C questions. You must start SH3 through Commander by using the tick mark far right or none of your Commander settings will take effect. Time compression is controlled via the rachet icon in the SH3 Options screen in Commander. As far as setting the game difficulty, as in auto targeting and whatnot, when you click on the big map to start a patrol there is an option at the bottom of the screen to change realism settings.
Finally, use the forum search feature, it's a Bilge Rat's best friend.