In a flyback transformer with multiple windings, how are voltages controlled for different current loads?
A multiple output flyback converter (with only one controller, i.e. PWM circuit/feedback loop) can only precisely control one voltage.  If you need multiple precisely controlled voltages, you will need multiple independent controllers.

That being said, in theory the output voltage of a flyback converter is dependent ONLY on the duty cycle and transformer ratios - NOT on the load current.  Unfortunately, this simple relationship breaks down because of losses, but in a well designed converter with fairly low loss components, the other output voltages should be close.  Whether they are close enough depends on your allowable voltage range and the detailed design of the converter.

Typically, multi-output flybacks make the assumption that they know approximately what the current draw of each of their outputs will be, and set the turns ratios to get close enough to the intended output voltage over the expected range of load currents.  However, all output voltages except the master output (whose voltage is being controlled) will vary over load conditions.