Bees are not a fussy as we are though. If they don't like the gap in your woodenware, they will seal it up.
When separating your supers and deeps, if you're easy with the hive tool and "ease" the boxes apart a little at a time, the pop will be more of a long crackling sound. As someone mentioned, a little smoke in the crack just let's them know you're there and they will appreciate that.