Well, the point of using the simulator right now is that (as I thought I'd understood from your first post up there) you wanted to know the relationships between different things. For that you don't really need to worry about overheating or matching it to what you have. You just setup a system, specify conditions like what you will encounter, and see how the system performs. Then change different things in the components to see how that affects the results, such as different winds of motors, or controllers with more or less current available, or batteries with higher or lower voltages, etc. You can also try different riding conditions with the setups to see how they respond, and then this can help you apply that to the setup you already have or want to get to know whether you'll need a bigger controller or a faster motor or a higher voltage battery or all three, etc.
Once you begin to see how the interactions work, then you can setup simulations of something resembling your proposed setup and conditions to see if it will do the job you need it to.
You can skip the relationship learning if you like and go right to the last part, if you don't want to learn how it works first, but it can be helpful.
Regarding the speed (or any other result) in teh sim, since you can't really directly simulate everything about a specific setup (unless the parts are already modelled and listed there), it's not always completely perfect. The way a specific motor in the sim is setup isn't shown anywhere on screen, so it's difficult to know if it's characteristics are really matching a motor you have, if theyr'e not the same motor. Part of it is the winding, the air gap, the magnet strength, stator lamination design, etc. Another part is how the controller commutates the motor and the phase current it supplies to it, and another part is actual voltage applied (including battery sag under load), as well as actual wheel size and any gearing between motor and wheel (none with a DD hubmotor in the wheel). Road conditions, rolling resistance, winds, etc., all contribute as well, though not as much as the others in most cases.
Thermal results that aren't modelled (no "overheat in" field) mean you can guess based on the efficiency field of the output / motor section below the chart. If the efficiency is low, then the difference in watts between the battery load and the motor load is being created as heat inside the motor. Any of that heat the motor can't get rid of will stay inside, and increase it's temperature over time, and it will overheat at some point. (this is what the thermal modelling part does automatically based on testing done for specific motors....for motors without it you have to guesstimate what the point is where heat buildup is faster than heat exchange).
But it is good for learning the relationships, and for guesstimating how things will perform. If you're using only parts already modelled in it, it's typically pretty close, sometimes nearly exact, in comparison to the real world results.
