I'm sure there's software that can track a conspicuous detail in video, but i did those tracking dots manually using "vector paint" in After Effects"

I paint a dot on the thing I want to track, advance one frame, paint another dot.... it only takes a few minutes and you will learn more about the motion by focusing on it that closely.

At animation Mentor they taught us to use a dry erase marker to put dots DIRECTLY ON THE SCREEN. :0 

Don't do that with an LCD monitor, it only works on CRTs.  Of course you can't save that, but the more trouble it is to do it the more you notice what's going on.

I read it's supposed to be back in in CS6.  I'd be surprised if there isn't some way to draw a mark on the screen somehow.

I thought Maya had paint effects.  You could import some video as a background plate and paint on it or some transparent layer in front of it? I don't use it anymore so i don't' know, but I recall there was a paint capability in it.

There's probably 100 ways to do it with other software too.   And check out Camaro's leads, they probably have something too.

There's a great program called Kinovea that can do something similar. It was originally for sport analysis but animators started using it so the creator is building in more animation centric tools into it. It's not perfect but it does a great job at tracking motion and you can manually track points too.

fading is just a preference, you can set it not to by going to Options > Preferences > Drawings > Persistence > and tick the Always visible tickbox