I find the best way to do it by far, is that while you're casting Animate Bone Minions, hover over where you expect them to come from. If you're correct (or just fast) then as the Minions spawn on top of each other, their name bars stack on top of each other, like so:
Bone Minion
Bone Minion
I hope you appreciate my textual graph. Oh yeah. So, I find the trick is to do that and click one, hit Death Nova, then click the other Minion and Death Nova him too. If you're quick you should have plenty of time before they move out of their 'birth' animation.
Apart from that... Just try to hover over where you think they are in the fight. I find the names most helpful. Hope that helps at least somewhat.
