objects won't allign on top of each other

I am building a long and complicated module with a lot of animation.  I have spent months on it, and am finally on the last part.... but it involves putting a ton of objects on slide and timing them perfectly but they need to be alligned perfectly on top of each other, and i can't get the formatting tool to get them to not appear staggered.  Has anyone had this problem?  The software also keeps freezing and I lose work...