seems like I've typed all this out at least three times before, but okay
There's two types of FB communication you should be concerned with.
First one is the Like (or Recommend) button. Think of that button as a sort of 'share' button (in fact there used to be a Share button, but its functionality has pretty much been folded into 'Like') You want a Like button on every page (or post) of your site that you would like people to share with their friends. Because when they 'Like' you, something shows up on their Facebook wall and their friends see it, and hopefully they'll come check it out too. If you are using something like WordPress, there are lots of plugins that will add this button for you. Once you get it up and running and start to get some traction, there are advanced options you can use to alter the display of the button, display a logo, give you stats and whatnot, but first, just get it going.
Personally I do not put a 'Like' button on every page of my site - it's not on the About page or the Advertise Here page or the Search Results page or anything that doesn't have content on it. There's no reason to have it there.
So the Like button is all about sharing the content that exists on your site.
The fan page is about bringing your content (and personality) to Facebook. I think of my Facebook fan page as almost a little mailing list. Anything I post there (and I am careful not to post too often or be too pushy) instantly gets pushed out to several thousand people. PLUS they can come to my page and interact with me (or with each other) My sites are usually event driven, and on my Facebook fan page, my fans post pictures and videos of the events, and talk to each other about the relative merits of the events, where to park, that sort of thing. I like to encourage that interaction, because it's building my community, but I don't necessarily want it taking place on my site.
The fan page is great for publishing updates to my site (I use one of the services that automatically publishes a link to my latest blog post to my fan page) but I also use it myself just to talk to people. I can survey them about what types of things they'd like to see on the site, and when I launched a new site, I had several thousand little evangelists that immediately spread the word for me. That was nice.
The facebook Fan badges (or the fan box) really only *need* to go on your home page, but if you have the room for it, stick it in the sidebar so it shows up throughout your site. And another pro tip - I use the Fan Box that shows the pictures of my fans in it. I hate how it looks, but I can't argue with results - when people see their own friends in the box, they are much more likely to click 'like' on it.
The Facebook fan page is all about bringing you and your message to Facebook.
So if you want to work your Facebook presence, you need to do it from two ends.
First is to have killer content that people want to 'Like' and share with their friends.
Second to use your fan page as though it was a personal mailing list, and show your fans that there's a real person behind the page.
Hope that helps. THIS IS THE LAST TIME I'M WRITING THIS. (ork ork)