Well, first of all, I'd suggest reading the User Documentation a Quick Start Guide, at least the chapters in which you have problems, e.g. Permissions.
Everything will make sense and is on a whole different level than phpBB2.
To your questions:
Warnings -> Moderator Control Panel - Warnings, there is a simple interface for all you need
User settings -> The user's settings will only be changed if the group your changing is his default one, you can change that via the User Management(and also set the settings individually there) or by the Group Management, where you can change it for more users at once.
Permissions are a bit more complicated -> Have you read at least the short descripition in the ACP on the first page od the Permissions tab? Don't have a clue then, look at the Documentation, i really don't think the mistake is on the phpBB side.