1. You can use a bee brush and brush them into the box
2. Use a flat surface, like your hive tool, or a spatula, and scoop n dip.
Not sure I understand your question - what do you mean swarm on natural comb. Bees don't generally make comb except in an enclosed area like inside a tree, or a BBQ or covered flower pot, etc. Post a picture of what you are talking about?