You are right, there is a low pressure swich on the system, so if ther is not enough freon in the system it will try and pump only the oil for the compressor, this would damage the compressor and possibly other components you will have to probably charge it a little, the reason why it looked empty on the guage is probably the section of line you are hooked on has the leak and there are check valves on the system preventing back flow which could in theory drain off one section. also water in the system is a possibility

The compressor has an electric clutch that clicks on and locks the clutch to the compressor. You will see it all spin as one assembly on the belt. It should click on and off about 4 times/minute.