V4 isn't hard to use. She's simple. As Richard points out above, the hidden magnets are just another way of doing JCM's like the gen3 figures have.
Loading a 'Magnetize' pose allows the magnets to be added to the clothing. Nothing you buy should have poke through if you are using limits when posing. If you are getting poke through, use the Magnetize pose and this should correct the issue. If it doesn't, I'd check to make sure you are loading the clothing correctly and following any instructions by the creator.

To answer the original question ...
If you have one V4, you use the first 'pose' file to magnetize and clothing you load onto that one V4. If you load a second V4, you use the second 'pose' file to magnetize the clothing, etc.
If it;s got no poke through you are worried about, don't bother magnetizing :)