Facebook experts pls verify this

I have a website fanpage. On my website I have a like button, like box, and now comments. With my implementation it appears that:

1) The like button only "likes" my url's and does not help my fanpage.

2) Comments from my website posted on facebook reference my website and also have nothing to do with my fanpage, unless I post from my website using my fanpage admin. (Other peoples comments do not help my fanpage, only my website).

3) The Like box on my website will add likes to my fanpage but does not help the website, outside of me promoting the website on my fanpage.

Is there a better way to tie my website to my fanpage using these?

You cannot make a like button for both your fan page and your site. Don't think you can find better ways to merge them, after all there's your site and there's the fan page, different things.

when you make the like button set the site URL to the fan page

I cant promise that works but its worth a shot

or replace the like button with another box with only the like button in it

Use this for your like box to have it like the fanpage:

<iframe src="http://www.facebook.com/plugins/likebox.php?href=http://FANPAGEURL.com&width=200&colorscheme=dark&show_faces=false&border_color&stream=false&header=false&height=62" scrolling="no" frameborder="0" style="border:none; overflow:hidden; width:200px; height:62px;" allowTransparency="true"></iframe>