1) You need to use logic gates. The way I used it is as follows:
It's slightly complicated, but if we for example take the fuel, I place the first gate, and make it read the fuel amount on the panel. The second gate is really close to only let one fuel at a time, and is reading the state of the first gate with the other panel, so that when the first one is closed, the second one is open and vise versa. For the ingredients it's basically the same, but instead of fuel level, you make it check if there's output. For something simpler you can actually check example images above, as provided by the creator of the game.
2) I've never had any problems with energy because I have this setup that always keeps my energies levels at an all high:
and if you need energy anywhere, just put a pylon or a substation there, and it should be good.
Hopefully this helps!