By micro I mean using them at a time chosen by me rather than just as soon as the antimatter reaches the required level. Say I was facing a Marza some frigates and some carriers, I wouldn't want my detonate antimatter or phase-out hull to autocast on the nearest carrier, I would want to keep them for when the Marza tries to use missile barrage, thus requiring a human element to time it correctly. Hence, micro.
Also, scout auto-explore is a given most of the time. Put it on when you first send them off and adjust their course for what you want if need be. They'll start off that way then inevitably go off and get themselves killed in a pirate base or something.