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There is a small edit button on the bottom left of the Top Sites view. With that clicked you can re-arrange your Top Sites.
You can also add websites to Top Sites via the Bookmark command (CMD+D).

Or do you mean something else?
 
You can drag the URL to the top sites window or another way of adding it is to select the bookmark menu bar and add bookmark for the page. When you do this, the next window that pops up has a selectable drop down menu and you can select top sites there and then do what Matthew suggests and use the edit button to move the top sites around or remove the ones you don't want.
 
Can't you just force it to be in Top Sites by visiting it often enough? That would make it, er, one of your top sites.
 
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