Obtain the Bomb Bag

^{Oops, It looks like I got the rooms mixed up.}

So the generator you're talking about is the one that is next to the room where you had to push a block on a switch to keep the windows open. These windows you could climb up out of. The one on the left has a ladder going down and the one on the right should give you access to the dinghy.

To get to the generator, you need to shift time to the present to disable those beams. However, you needed to be in the past to get to the room in the first place. You need to shift back to the present from there. How do you do it?

Well you need to lower the dinghy so you can reach the deck and hit the crystal. From that room, it would be easier to just climb out the window with the ladder, go down and and look toward the other window and up at the deck. You should see the dinghy there with a target to hit. Hitting it will lower/raise it.

After you had lowered it, you can return and climb onto it and hit the target again to raise you to the deck. From there, shoot the time crystal to shift to the present. Then you could return to that room using the dinghy and to the generator. Now you need to shift back to the past again so you can activate the generator. Fortunately there's a grate above with a clear view to the time crystal. Shoot it so you can shift to the past and finally activate the generator.

To get to the second generator (the one in the south), start off from the first generator.

You'll notice that the room across the hall on the left has a fan in there. If you are in the past (everything is colorful and operational), the fan should be spinning. Inside that room, you should see a blue switch that you'd have to shoot at. You cannot shoot through the fan when it's off so you need to go to the present (where everything is dull and not working) and shoot it then. That should open the door to enter the room (IIRC).

In the room there should be a switch on your left and bars on the right looking into the next room with a box sitting on a platform. The switch opens a hatch that covers a target that you have to shoot at however you don't have a direct line of sight to it since the box is in the way. You'll need to move the box over so you have access to the fan behind it. You need to open that hatch and shoot at the target. With the box out of the way (and the fan off), you should be able to do so. It should open the gate leading to that room.

Now you have access to the generator so you just have to go back into the past where it's operational and turn it on. You can access the crystal back in the room with the previous generator.

They serve no purpose, they are just merely the skylights for the houses they are above. Notice at night, it is a lot brighter from the outside. That's because of the lights inside shining out. If you look from the inside, it should be pretty clear that they are skylights:

Skylights at night from inside Kukiel's house

They are probably all designed that way to go with the Skyloft theme of having fans (and fan-shaped objects) everywhere.