I’m just beginning with WP myself, so these may not be “high quality” ideas. But…
Do you know about the Firebug plugin for Firefox? I have found it very helpful for discovering what styling is affecting some part of a page.
As far as where to change the code, I’m going to say “Themes.” In your WordPress installation directory, there is a “wp-content” folder and inside that I “themes” folder that contains a folder for ever theme. You may not want to directly edit the stuff in a theme folder, but I found looking at the contents to be helpful.
Also, in the Dashboard of your WP install, click “Appearance,” then “Editor.” Here you can edit the text of any of the files that make up the current Theme. Something I’m currently unsure about: If I change any of the theme files, how do I preserve this customization?
A few Codex sections that I found helpful:
Using Themes
Stepping Into Templates
Template Hierarchy
The Loop
