BMP and JPG files cannot save layers. You need to find a good graphics program that is worth your time to learn. Photoshop and Paint Shop Pro are probably the two best, but there are numerous others. Try out different programs before you decide in which one to invest HUGE amounts of time.
There is no one tutorial out there for everyone, because doing repaints is a very creative venture, and creative people will always come up with their own ways of doing things. It's more about learning a specific graphics program that you feel is worth years of your life to learn. You can almost master most of the elements of repainting in less than a year, but if doing graphics is a passion of yours then you will always be learning something new every week for the rest of your life - not from someone else, but from your own imagination and creativity.

Does that help to explain why learning repainting is so elusive? There may be wrong ways to do things, but there is no single right way to do graphics. It's up to the individual's tastes and imagination. That is why it sucks for a beginner looking for one set of answers - there isn't one.