Can the captain of the vessel choose which attacks get stopped by the void shields?

lets say i have 2 shields, and they attack me with a battery and a lance, can i choose to remove only one die to the battery in order to stop the lance or all the shields go down with the first shot of the batteries?

The attacker gets to choose what weapon to shoot first and damage is applied first come first serve. Raising and lowering the shields happens at the beginning of the turn iirc. So yah he can use the macrobattery to drop your shields.

If you have the Hostile acquisitions book there is a upgrade called overload shield capacitors or some such, which lets you bring your shields back up to strength after they have been dropped. That might help.