Saph from the Hellhades team did a video on this awhile ago if you haven't seen it (https://www.youtube.com/watch?v=l70DxSfY4ic) but in a nutshell it boils down to a couple of things:

• Finding the target with the lowest HP
• Finding the weak affinity if that matters (i.e. CB isn't void)
• Finding targets with no increase defense, block damage or counter-attack
• Finding the target with the lowest HP % left (i.e. usually someone with low defense and high HP) 

It is funny that you mention Skullcrusher, as I have always found in my setups that he always took the stun, regardless of what I did.  Even if I made someone else have ridiculously low defense and HP (or even high HP), CB always seemed to be afraid of the counterattack buff

The steadfast mastery also appears to be an avoidance for CB, so putting this on all champions except for Skullcrusher can also help

Thank you :)