I think the easier way is the way they have it. You don't do anything but have patience. After a day the top sites has read your mind and they are all in there. Now that they are you can just go to edit and thumbtack the ones you want permanently. Hopefully the ones you never want in there are permanently deleted and never return after you have Xed them.
The reload button isn't missing, it's at the far right side of the URL/Address input box, as is the stop button.
However, if you want "real" buttons back, as well as the progress bar behind the URL as it used to be in Safari, just type these two commands into the Terminal app:
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