Once you assume that program cannot be fully trusted, you are already on right path.
I belong to the "older gard" who did almost everything by hand at least on few small projects, and now I see young engineers who seem to be completely relying on pressing software buttons, which goes really close to driving car by looking at the map without taking a look through windshield.
The main problem is that there is less and less effort to provide basic eduction on that through regular courses that are inclined to provide very generic and oversimplified explanations.
That is why Autokad's desire to learn about process is really smart.
ASHRAE Fundamentals book gives exact overview of the process, and I would recommend that you do it manually for several typical rooms, but to avoid too many repetitions as once you get a grasp of process, you can spend your time better by reviewing software results and comparing them.
Personally, I have more trouble currently with infiltration issues for residential projects than with anything else.
After you finish several projects for your frequent location, you will have many data about losses/gains per area and orientation both for outer walls/roofs and glasses with some typical SHGF, interior loads as well, but infiltration is real burden and you actually need to assess it.