Synthetic queen

Just got the synthetic queen...
Shes destroyed 2 of the fallen empires, I got farqlans head and the empire that I get ships from actually is awakened (and NOT cracking planets, thankfully).
They actually seem to be fending her off too... shes lost her starting territory next to them...

though, I noticed one of their systems says its owned by her (even though its still their territory). Hard to say whats going on considering her whole nanite miasma crap.
I'm just waiting for the second situation research so I can jump in and help defend my pet fallen empire (love that I can say that)....

In the mean time, how should I best prepare?

Is there anything I'm missing by jumping into war against her?

Is there a recommended guide or method people recommend for how to go about the whole situation with her? I know shes eventually going to turn on us... shes looking to end all sentient life... so eventually ill have to fight her.

Also, I saw in the wiki that theres a synthetic apprentice thing? Whats that all about?