Yes, the low side/end has a yellow light indicator. My system is "automatic" in that I press the "level" button and it goes to work. My understanding is that it first lowers the two jacks on the lowest end together, then lowers the jacks on the lower side together. I can manually raise or lower jacks, but when I press a side or end up or down button I am controlling two jacks at a time on that side or end. That is to reduce the possibility of twisting the frame and popping windshields, etc out!!!
I would presume that if you have a manual system, you first have to level one direction, and then the other. What that means about having all 4 jacks down, I can't say, as I have experience only with the comptuterized automatic system. The automatic system does complete it's work with all jacks on the ground.
And yes, after the system has done it's automatic computerized leveling, it may not be "level" depending on what you check as a reference. (You might find the floor to be different from a counter top if you check with your level...). We normally open the shower and bathroom doors to verify it is "level" ...if they do not swing open or closed on their own, we are declare it to be "level." We often tweak one side up a "bump" or two to get it level to our satisfaction. The level sensor can be adjusted, but we have never bothered with trying that.