Meanwhile: Did you notice that the NEI display in the video's thumbnail is saying "invalid structure"?
I did notice that. It is because you have the smeltery controller turned sideways. Since I haven't had time to watch the video yet, I thought that you might have fixed the problem. As far as I know only the drain and the controller have to be positioned correctly and the drain only needs the small hole to be facing an outside wall. The large hole in the back is nothing but decoration. Meaning that it can drain from more than one side if placed right.
Also, if you haven't thought of it already, add an extrautilies clock---on the OUTSIDE---next the drain channel. It will pulse the channel once a second to pull the molten metal out of the smeltery unless it receives a redstone signal. A hopper can pull items from the table an into a chest. Voila! caveman automation.
As for my preference for the 3x3, most blocks must be made from 9 items. So for metals, a full smeltery (1 layer, 3x3) makes 2 blocks. And double compressed cobble can be used instead of plain cobble. You just have to remember to used an even-numbered amount otherwise your ingot-cast or basin gets jammed up by not filling completely.