Each application will have instructions on how to send the letters. You should ask the same two people to send letters to all the schools. Do not ask them to make copies — let them figure out what to do. Most will print out a letter and attach it to the form. Many schools now have the process on-line — so your references can cut and paste their letters onto the screen.
You are wrong that MOST schools ask for one academic letter and one professional. The top MBA programs want you to have three to five years of work experience and would prefer both to be from people with whom you worked. When I applied to MBA programs, they only wanted professional references. Read the instructions carefully