So, I’m trying to bake this protein bar in Substance Painter, but I’m having difficulties… The baked textures look pretty bad - very patchy and none of the modeled detail is there.
I tried to make a custom cage that covers the whole low poly model but that didn’t do much good.
Also, the thin flaps at the ends of the model seems to become one sided (it becomes transparent from below), but there has to be a way to do this without giving the flaps on the low poly model thickness, right?
If I do, I think I will divide it into 1 and 2 and combine it into one after two bake. 
Since UV has mesh-specific area, combining after baking 2 is not a difficult problem.
Could you clarify how you would divide it?
I forgot to attach the image. 
The problematic part is the overlapping part of the wrapping paper on the back, so I think you only need to separate that part.
Alternatively, you can restore the problematic area under the overlap by replicating it with an image of another part.
Somethings you can try and test. You can share your UV map or high poly model screenshot.
Make the end flat and bake it. Then deform or bend the end.
Add one or more seams near the end or on sides.
Add some thickness, bake it and remove the extra faces no longer needed.
You could also bake different parts separatly, with the help of a Mask modifier…
But it’s difficult to say without seeing the UV layout, and both Hi and Lo res models.
