Don't apologize for the questions. It's why you subscribed. We're thankful for that, and ready and willing to help however we can. Thank you!
1) There's a few ways to do this. We'd recommend downloading and installing the JFBCContent plugin. This has the option to add a Like and/or Comment box to every article on your site. This plugin will also be installed by default with the 3.2 extension coming out next week, and will have a lot more configuration options as to which section, category, or article it will show it. If you're interested more in the 3.2 release, see our sneak peek blog post:
www.sourcecoast.com/blog/item/106-jfbconnect-32-sneak-peek
Don't worry, everything should work just like normal when you install it, so your configuration now won't go to waste.. there will just be a lot more stuff to play with then too
2) We have a JFBCFan module that you can install and use. It should let you configure it similar to how you configured the code you got from Facebook. If you'd prefer to use what you already had (your code), you can. The code that facebook provides has a script inclusion like <script href="...all.js". Simply remove that line, and it shouldn't interfere with JFBConnect anymore. We already include that file.
Hope that helps, but if not, let us know and we'll get you going!