I can answer a couple of your questions
2. Yes, you must verify the population. The BIs are your challenges during your validation and the population is used to determine your Fo. You want to prove that the spore population is as the certificate says to prove the kill time is adequate. For steam sterilization a population of 10-6 is required
3. You must follow your validated load patterns during routine operation. When developing your cycle the “worst case” equipment should be determined and minimum and maximum loads should be verified. This way you don’t need to use the entire contents during routine processing. But the location of item that are in a load pattern must stay the same