Do helium and lighter gasses rotate with the earth or do they go slower

Like, there's nothing holding them back so you'd think it would go slower. Same for there being some difference between the top of the ocean and the very bottom. Like a lag or more sluggish at the top.

What I was thinking is. Maybe the top of the atmosphere is actually a lot younger since they go around slower and that's why your burning up when you re-enter the atmosphere, it's some kind of distortional effects of that.

No. In fact helium moves faster than most atoms because they are lighter (helium is the second lightest element after hydrogen). Helium atoms move fast enough (at the temperatures we experience at our distance from the sun) to escape Earth's gravity entirely.

So now that you know about the first part, your second part falls apart completely. And burning up in our atmosphere is caused by friction. No fancy theory about it.

Please read about known facts before proposing a hypothesis out of the blue.