In short (regarding Manual mode), once you fiddle with fan speed and temperature and outside air button, the AUTO light turns off and you are essentially in Manual mode.
In most cars it stays that way upon restart too, which is how I prefer to operate the climate control system on a daily basis. Sometimes I get my car back from service at Lexus dealership and it's in AUTO mode, but once I fiddle with fan speed, temperature, etc. it goes into manual mode until somebody hits AUTO button again.
The side effect of this mode of operation on regular basis is no stinky ventilation system. It's worked for me in several vehicles equipped with climate control systems (including Lexus, Mercedes, Jag, Porsche).