I keep all balls in play and only trap a ball for a wait on a specific shot. Multiball can be a mayhem of shots as balls knock each other so sometimes specific shots can stuff up.
I find it best not to focus on the flippers but keep your eyes about mid field to keep multiballs in play longer.
The way you play multiballs also depends on the machine you play. On earlier machines it was much more difficult to get and then keep multiball in play.