Ace, I am still real new to the Orbiter too, so do not take my brief explanation as THE answer. I am only trying to give you the concept behind it. Also I am at work so I am doing this from memory.
I use the Sync when I am in essential the same orbit as some object, like the ISS, but my ship is either ahead or behind the object. First you have to select your target, but you can only select a target that you have some kind of intersection with. That is to say somewhere the two orbits must cross the same spot.
Next, look to see if you are in front of the object or behind the object. If you are in front of it you have to slow down. And how do you do that? You make your orbit bigger. But how big you ask? That is where the sync comes in. If I remember right there are three modes. They are something like ApD/PeD, Intersection and Manual. I usually just use Intersection because I am real lazy about aliening axis. So anyway the dark green line is the point you want to intercept the object at and the times on the right show the time you and the object hit that point on each orbit.
So with the problem of the object being behind you, you need to do a prograde fire to increase the size of your orbit so that your orbital period is longer than the object's. But you want to do this so that one of the orbits on the right has almost identical times.
Then when you get to that point at the correct orbit the object will be right there and you can fire retrograde to match periods.
I hope this helps and doesn't just confuse you more.
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