There is no good way to prune Crypts, or, for that matter, all crown plants. If your crypts need pruning, you should probably take them out completely because they are too large for your aquascaping plans. Either try smaller crypts, or a different kind of plant alltogether, that either grows or can be pruned to your specifications. You have to plan ahead with crown plants and envision what they will look like when they reach full size. If a patch of crypts is advancing by means of runners into territory where you don't want them, you can pull up the newer plants and confine the older ones to where they belong without hurting the older plants.