I don't know exactly what piece of information you're missing, but stomping when the fireflies are above and to the right of Toki will send them to the top right direction.

Yeah I know stomping gets them to fly up, but for them to deactivate the skull thing they need to be lit by getting close enough to the firefly in the cage and I can't seem to do that without waking up the bats who then attack me. They seem to only fly directly up rather than off at an angle.

If you are not directly under them when stomping they should fly up at an angle.

Thanks for the reply :) I will have to try again, I thought it would be some little thing that I wasn't doing quite right!

*replying after 2 years and a half*

I saw your achievements, and I noticed you never finished the game.
Anyways, for this situation you have to send the flies towards the cage (where they will lit) by stomping and pushing them right above you. To do this, you need to whistle right below the cage so the flies will be positioned perfect for you to push them up with your stomp. The problem is that when you whistle or stomp(not sure about this last one) that close to the bats you will wake them up and force them to attack you. To deal with this, after you whistle, you have to head left immediately towards the water that is falling. Get behind it, and the bats wont be able to go through it. Then you just wait until they go back to sleep.

I know there are several mechanics that the game doesnt explain to you, but this is what this game is all about. Figuring out how the game works without handholding like almost all modern games do.

Place the fireflies by chirping in the place where the sound of chirping is near to bats, but doesn't awake them (bottom of the ladder). Then, move 1 step left and stomp (firefly will be moved up-right, angle about 60 degrees.
Then, climb up the ladder. After that chirp while falling down to the left of the ladder. Place the firefly at the bottom of the ladder, be there, too, and stomp.