Don't feel like an idiot - trust me... that's a normal question! And plugins are (for the most part) easy peasy compared to file permissions! In fact, don't mess with file permissions too much, or you might find your site disappears on ya!
File permissions (664, 755, 777, etc) have nothing to do with the way your site appears on the web (unless you use file permissions to stop it (or parts of it) from appearing on the web) The only thing is that if your permissions are set too high, it makes it easier for someone to "hack" into your site (which oftentimes is never really a big deal, most do it just because they can - so don't sweat that too much unless you've got a hacker that really hates you) ;) But file permissions are server-side (FTP rules/permissions) and your web site is something the display of what's on your server. Does that make better sense?
The default is that people can read and comment, as well as use trackbacks and pingbacks to your site. So if you see a comment that doesn't look like the others, (might have
[...] at the beginning and end) that's just someone linking to you.
Here's a good reference link - it's the WP "bible" so to speak: http://codex.wordpress.org/Main_Page