The fact your machine is new with very little in the way of third party apps installed, actually argues against a clean install.
The idea of a clean install is it gets rid of remnants of old apps you may have installed and not completely deleted properly. If you have a new machine you have not installed much of anything on there, you really are wasting your time with a clean install.
Time Machine backs up the entire drive including the OS. So how ever much space your entire disk is now using, a TM backup would use that amount. A USB key will work for this, but is not ideal. Those USB keys tend to have low end controllers in them and cheap memory chips, making them unreliable for long term backup usually. If that is all you have now, it is better than nothing. But long term you should get yourself an external hard drive for this.
An SMC reset will not likely fix that app. I would not be surprised it that app won't work at all under El Capitan. El Capitan implements some new security measures that restrict ways certain third party kext files can access the system, and most of those temp apps use a kext file to access the temp readouts.
Is there some problem you are having that you want to run such an app? I would just delete than thing and ignore the temps. If your Mac overheats it will shut itself down.