Internal or external drive makes virtually no difference. The CPU and GPU generate the heat.
There is no need for SMC Fan Control as the SMC already controls the fan properly. You can expect the Retina display to generate more heat rather than less although Apple runs the display at a lower light level to reduce the power needed for backlighting the display. But before you start worrying about it why don't you wait to see if you even have a problem. You're being a bit premature.
Your external drive will have no affect on the heat, it comes mostly from the CPU and GPU, but from other components as well.
Some older models of Macs it was good to use SMCFanControl because Apple thought it was perfectly fine for the CPU to get over 100º C before even starting to spin the fans up...
I've found on my Retina model, not only is the cooling designed much better, the fans react much quicker, and I don't really think SMCFanControl is needed.
I hope the creator updates it though, just cause... I've been glancing through the source code, but I haven't figured out the root of the problem yet for finding the Temp.