if I understand your question correctly then the answer is this:
Virtually everything in Aurora can be done automatically. So in my current game, I have given a survey fleet the order "Go through 3 jump gates, and enter the 61 Cygni system. Once there begin surveying 61 Cygni I, then II, then III, then IV and moons IV A and IV B, then V, then moons V A, V B, V C....and so on. It will take them like, 2 years to do all that.
In that time, I can advance time however I please. I can advance time in 5 second incriments to micromanage a fleet arrangement before battle, or I can advance time by 30 days, then 30 days again, then 30 days again, to quickly advance until i have some technology researched.
If something interferes with your fleet's progress, there's a good chance the game will STOP its operations. Steve has done an excellent job setting it up so that petty much any time you WOULD like the game to stop, it will. So like if my survey fleet suddenly spots a strange thermal signature orbiting 61 Cyngi V during the 5th day of a 30 day cycle, the game will stop its time advance. This will happen pretty much any time a new spaceship is detected, a spaceship blows up or finishes doing something...ect.