Controlling multiple output pins....

I have a question on how the Arduino (or most other controllers work).

So, if i wanted to use the analog outputs to control multiple things, do the outputs shut off as soon as the code no longer runs that line?

For example, I wanted to use PWM for temp control in area 1. It goes through the loop to maintain temp for area 1 with the PWM output. When I move into the loop that monitors and controls other areas, would the analog output stop for area 1 since the code is no longer using the analogueWrite command for that pin?

The outputs stay as you set them until you explicitly change the state of their output (another analogWrite or digitalWrite).