To respond to my own post and for posterity's sake...
Using the forum search function I found an old post from Carl with Songbird (http://atariage.com/forums/topic/226894-total-carnage-pro-controller-compatibility/?hl=total+carnage&do=findComment&comment=3189231). How meta is that! You should use the forum search just as I should have done before I posted this... Anyways it appears B&C, and not A, are used on the standard controller. B to hold position and fire and C to drop a bomb.
Hope this helps any future generations after the Morlocks take over.