Tuning gives you the option to adjust the base frequency of Audiotool. The default is 440Hz which is common in all DAWs. Changing the base frequency will affect all instruments that process notes.
Microtuning provides you an option to locally adjust the tuning of each key within an octave (in cents). You can create as many Microtunig sets as you want and choose in a synthesisers context menu which to use.