Used them like you suggested but felt better with soil top to bottom.

To make pot soil aeration and keep it's springiness bark fibres and long strands of organic material seem to be best. Soil just compacts round perlite and clay balls. My soil has all that I wouldn't need more so buying a pre made soil for your individual needs is a lot better than mixing yourself.

Potting up is much better as roots drain soil the best so once you have established roots watering is much less scary. Going into a big final pot with a week old seedling isn't the easiest or best route but people do it so I'm not going to call it bad just needs more work around.