The motion tracking of the lion works pretty well but I'm not seeing anything where your son runs in front of the lion. I assume you just left that part out of the YouTube clip?
The reason it didn't work when you put the lion layer under the main layer is that the program doesn't "see" a boy, grass, and a lion. Just pixels of different colors and luminosities. Think of it as a photograph instead of a video. If you have a photo of your yard and you want to paste a cutout of a lion on top of it, it will work. Paste the entire photo on top of the cutout... and you see the whole picture and nothing of the cut out.
Now say you wanted to paste the cutout of the lion into the photo but in the "background" while a boy is in the "foreground." What would you do with the lion cutout? You would further trim the lion down in the shape of the boy's head in the foreground so it appears to be behind him.
That's exactly what you need to do with your video. Cut out the shape of your son's head from the lion using a Mask. The only difference is that it is animated instead of a still frame photograph. So this requires that your mask adjusts frame by frame so it only cuts out your son's shape exactly, each frame, to give the illusion that the boy is in the foreground and the lion is in the background.
-- Choose the layer with the Lion photo (very important you are on correct layer)
-- Use the Pen tool (G key) to create a polygon that covers the area of the lion that is obscuring your son's head. Once closed, the image will default to a cutout of just the area within the polygonal mask.
-- If you haven't already, expand the Lion layer by hitting the triangle button. You already see a line that says Tracker, and a new line that says Masks. Expand that line as well.
-- You will see a sub line that says Mask 1 along with a drop down box that by default is set to "Add" as well as an unchecked box that says Inverted. You have two choices here, both do the same thing. Either check the "Inverted" box, or click on "Add" and change it to "Subtract."
--Either way, it should show the whole lion, minus the part that is supposed to be "covered" by your son's head. But you aren't done yet.
-- Further expand Mask 1 and you will see more options. The only one you need to worry about for now is Mask Path.
-- Click the Stopwatch button to create a Key Frame. Key Frames are what will allow the mask to animate along with your son's movements.
-- Advance the video by one frame. You will see that the boy has moved but the mask has not. But if you click and drag one of the polygonal points from the mask, it will move and alter the shape of the mask. It will also create a new key frame. Be careful just to move one point and not accidentally select and move the entire mask. If you do that just hit Undo and try again. Adjust as many points as necessary to maintain the proper shape of the mask around his head.
-- You must continue this process frame by frame for all the frames where you need to mask out part of the lion.
-- There may be frames where, due to motion blur, there is not a hard edge of the boy's head to cut the mask on exactly. In this case, try to experiment with Mask Feather to try to blend the edge of the Mask within the motion blur of his head until it looks natural.
That should solve your problem.