To make that more obvious:
For manufacturing bonuses, use factories. Power plants and your manufacturing capitol gain NO benefit from these tiles.
The same goes for research. Build labs on the bonus; tech capitol and research coordination centers gain NO bonus.
Build farms on food bonus tiles, but be careful. Morale on the planet is linked to population, and it is very difficult to support more than ~20 billion people per planet. Avoid the 300% bonuses, they often cause overpopulation problems.
Morale and influence bonuses can be used for any building that gives a percent bonus TO THAT PLANET. Things like trade goods (harmony crystals, etc) or the Restaurant of Eternity that give bonuses to your entire empire do NOT gain any benefit from the bonus.