By piping stuff into the controller. One can just put a hopper over it and a chest over the hopper in the setup I showed above. Alternatively an AE system should hook up to it just fine. The one caveat is that dealing with multiple types of stuff can be a bit tricky if you want to avoid making alloys. I tend to avoid fully automating it for ore processing in favor of the more traditional pulverizer/furnace setup.
There are little tricks that can make doing an automated setup a bit easier. Liquid routers and other various liquid filtering/sorting solutions could work well. Casting tables, basins, and liquiducts can only hold one liquid at a time, so they can work well together. Filtering/sorting pipes (such as emerald pipe) or precision import buses can be used with casting tables to remove ingots without removing the cast. Liquid metals can be pumped out of casting tables/basins as well as back into a drain to refill the smeltery. Have two liquid metals but want the alloy they make? Pump them into the smeltery drain (assuming the smeltery isn't totally full of liquid) and they'll combine as much as they can.
To avoid making alloys, you could use two smelteries. One for copper, cobalt, silver, and ferrous ores (and obsidian if you plan to melt any of that down), and another for everything else. That should avoid all of the TiCo and TE alloys, as far as I know.
You can put hoppers underneath casting tables, which will automatically pick up the ingots so you only need one import bus on a chest at the end of the line of hoppers. If you have the resources for it, you can also use liquid logistics pipes to pump liquid metals back into your smeltery to make alloys (although I wouldn't recommend them for pumping liquids OUT of a smeltery since they aren't very fast).
