Default CSS / Standard Directory Set Up
I'd agree with trying the theme suggestion in the above comment, but if you do want to change css I would use "extras.css". See the hilited box on this page:
https://wiki.civicrm.org/confluence/display/CRMDOC/Resource+URLs


  "You can also define additional CSS styles to be applied to all or
  specific page elements by adding CSS styles to the 'extra CSS' file:
  css/extras.css. This file is included in the downloaded code, but is
  empty by default."


It's difficult to answer the other questions because they're a little too general.