ethan,
you have many questions. that is good. i will try to answer as many as i can:
Could they of not put enough refridgerant in the system?
there is the possibility of what is called an undercharge. this is a lack of freon in the system. i cannot tell you unless i have my tools and myself at the scene.
Don`t these systems come pre-charged with refridgerant?
yes, most systems come pre charged, to a point. the factory assumes that a certain amount of freon will be needed. this might be 5 ounces or 20 pounds. it just depends on a lot of factors. its also easier to explain in person
Do tech need to add to what is there?
as to the above question, sometimes and sometimes not, it just depends
Have I damaged the compressor allowing it to run 6 hours continuously??
absolutley not. your compressor is just fine if the charge is close to correct. in a heat pump in winter, some compressors will run 24 / 7. your service tech can help you better with these ???'s!