As you get to be more advanced in this game, with more dwellers inside of your vault, you will unlock a greater variety of rooms, which earn you far more food, water, or power as compared to the other ones. The nuclear reactor is used to produce greater amounts of power. The garden will earn you more food, while the water purification room will earn you more (surprise!) water. The Nuka-Cola bottler will earn you both food AND water.
The same thing is true with these as was true with the old rooms. You can earn more at a time if you double and triple the size of the rooms by merging identical ones together. If you are going to merge rooms, which you should, then merge them before you start upgrading, not after. If you want to make room for the new rooms, then sell/delete your old rooms and replace them with the new ones. Just make sure you have the caps to do so.
Make good use of the weight room, the armory and the athletics room. The weight room trains the strength of your dwellers, which helps in the power generator and the nuclear reactor. The athletics room trains the agility, which improves the performance of dwellers inside of the restaurants/diners and the gardens. The armory trains perceptions, which helps inside of the water generator and the water purification rooms.
If you want to get rid of some of the dwellers temporary so that you can get out of the red bars and into the blue bars, the easiest way to do so is to send as many of them on missions to the wasteland as possible. When they are in the wasteland they will require no food and no water. Use this time to build up, and when they return, you can keep them out for as long as you want to before letting them back in. Or just let them explore for awhile.
Get the dwellers out of the rooms if their SPECIAL stats are not conducive to the room. Their unhappiness will actually degrade the performance of the room and end up costing you more power/water/food than their position in the room is worth. If they have a stat of 1, either equip them with an outfit that improves the stat, send them to the weight room/athletic room/armory, or send them elsewhere.
Dwellers will cost less food and water if they are in the living quarters rather than in a work area, too, so if you want to get some of them eating and drinking less, send ’em there. Even when they start making babies, this is a good way to save resources and get the bars up well into the greens.