Fit it just like the mod is, linearly aligned with the fan ducts aka on top of the heat-sinks. The idea of the mod is to get most air through the heatsinks rather than escaping through the sides and top.
I am assuming here that it is a temporary fix as card-board can be a fire hazard IF the the dreaded S5 overheat bug hits you.
Ok - so I've fit it pretty well I have to say. On top, its going from the very front, under the cpu/mobo, then all the way to the end. The bottom is similarly covered to the mod, without the bulge obviously.
Temps are
64° / 60°, so unfortunately it doesn't seem to have helped.
I live in a very hot country and during the day there's no A/C so room temp will be pretty warm, not sure if I'm comfortable leaving it running if I'm getting these temps in an AC'd room

Maybe I could manage it remotely and underclock if it gets too hot?