Second question is easiest - you make a user a site-wide admin by adding them to the "system administrators" user group.
As far as the first question, administration in the ACS has been an evolutionary thing, with various modules taking different approaches based on when they were written (usually for a specific client of Ars Digita). So there's a woeful lack of consistency. The doc pages for each module should talk about module administration.
Cleaning this up and presenting a uniform administration style is one of the goals of ACS 4.0.
