What you want to do is align the blade to the miter slot (I use the left one). That way you will get accurate crosscuts. To do it, yes you have to loosen the trunion bolts until they're just snug and tap the edge of the tabletop with a rubber or dead blow mallet to align it. Easier than it sounds, especially with a cabinet saw.
Once the blade is aligned to the miter slot, then align the rip fence to the blade.