The pages in my booklet don't line up correctly---ahh help!!

Check the X coodinates in the upper left corner and make sure the art is placed or drawn to the guides or edges. A little more infomation would be extremely helpful.
Another thing to do is turn on the Overprint Preview. This is in the View menu. When you turn this on, you see how exactly things are placed/lining up instead of a low rez screen preview.
Are you converting a Publisher file to InDesign? If so, you will HAVE to fix this. Not an exact science. Even with the Utility, they are 2 totally different apps. InDesign will do it's best to maintain the look of the Publisher file, but Publisher was not created for high-end output, it has gotten better over the years... but it is still THE most problematic software for Printing.