Vin;
For what it's worth, I lap sanded my base box both before I glued on the top, and after, to prepare the bottom for mating with the base. I'm sure Fergy will address this, but my limited experience with this is that if the joints don't match up exactly, or least as close as you can see, there will be problem with the joint.
I see you're in Albany, my home town. I've lived in San Antonio for many years, but I still miss the northeast.
Matt