1) When using the JFBCLike tag, you can pass the URL of the page that is meant to be Liked. This can be your home page (for use throughout your site), the page of a specific article, or even a Facebook Fan page. You can choose. If you leave the url= parameter blank, the tag will default to whatever page it's being displayed on.
2) Things to watch out for: If you don't have sh404 (or some other SEF component), if you just use the tag with no url parameter on an article, it's possible the user could arrive to that article through:
index.php?option=com_content&id=20
/2-category/21-article
A blog view showing many articles
Because of this, the like button on both pages would be 'different' to Facebook. If you use the url= parameter and force it to the 2nd (SEF) url, that guarantees that wherever the Like button is shown, it will refer to where you want it to.
3) No great tutorials, sorry. We'll be revamping our documentation over the next few weeks to prepare for 3.2 as well as incorporate suggestions like this. Feel free to ask away, and sorry for the trouble.
4) There was no #4
5) Yes, if you're using 2 columns, sometimes things overlap. There's a little flexibility we have with sizing these things, so if you want us to look into it, let us know. The FB widgets in general use Javascript and iFrames, which can cause overlap issues.. and just isn't always easy to fix, unfortunately.
6) Using absolute positions would definitely cause some problems. You may be able to use relative though, which would allow you to always shift the box up by 20px and to the left by 10 from wherever we put it in by default. Worth a shot, but still may not fix everything.
Let us know what we can do, or where you need more info!
Thanks!