I've gone through a couple of jobs that I could have used this. Let me know if this works for you. 
I've only tested this script with maya 2011 but it should be good with older versions too.

DESCRIPTION:

First:

This script enables you to create a boolean with one master object and as many receiver objects as you like.

It will also provide you with a controler for the master object.

 

Second:

If you select "keep animatable". Both Master and receiver objects can still be animated after the boolean is applied.

 

Third:

You can still apply the boolean to a previous boolean and still edit the parts.

 

INSTALATION: Install script in usual scripts directory. Source Script: "fRayBooleanMaster".

HOW TO USE:

>> OBS: Your models need to be closed for the booleans to function properly! <<

 

 

1. Select what type of boolean you want (you can change this option at any time before you select your "finalize" option).

2. Select the object that will affect all others.

3. Select objects you want to affect.

4. Choose weather you want to keep your objects editable with "keep animatable" or if you want to delete history with "finalize boolean".

 

FOR ANIMATING:

 

1. When Editing or Animating the Master object just move the objects inside of the "CNTRL_objs_grp". You can select them directly or through the

display layers created for them.

 

2. You can also edit or animate the Receiver Objects by selecting them inside of "receiverObjsGRP".

 

LIMITATIONS:

 

When INT option is applied. And afterwards when your moving your controler; If its not on top of some of the receiver objects

your command line might show this message: "Warning: Cannot perform boolean operation". This will not have any effect on your boolean.

 

Only the Master object's Shader will be kept when the boolean is applied. Receiver obj shaders can be edited afterwards.