Badger, this is only tangentially related to the initial question, but might be of interest to the original poster anyway so I'll leave it here (but please consider starting a *new* topic unless your question is directly related to the initial question).
Generally speaking you would not want to "tonemap" a render element, although you might adjust a specific one to get a particular effect on the final output. For example let's say you have your Atmosphere element and you want a redder atmosphere, you could redden the atmosphere. Or if you wanted more indirect light, you could increase brightness of the indirect light element. This of course only works properly after you have reassembled the elements in the correct way to reproduce the look of the normal output. The render elements just give you more power to adjust individual scene elements like clouds and atmosphere *separately* from the ground, say. That kind of thing is nearly impossible with just a single, non-layered image (i.e. with no render "elements").
Using a literal "tonemapping" tool (in the modern software feature sense of that word) on a single render element is unlikely to produce good results. If you must use tonemapping, do it on the final composited high dynamic range image. If *all* you want to do is tonemapping, don't bother with render elements, just output the final render to EXR (the Save As dialog on the normal render window will do this), and then tonemap your EXR in whatever your favorite tonemapping app is.
So short answer: render elements are for compositing and very specific adjustments to individual scene elements. They are not generally for normal color correction, tonemapping, etc, etc.
- Oshyan