Aadsas has a whole Q&A to answer all these questions.
You input the grades exactly as written from your official transcript.
You input the retakes by the semester you took them. Exactly as written on your transcript. You can select both courses when choosing prereqs for the schools when applying to them in the app.
you should input different transcripts grades from different schools separately.
You will put 2 transcripts on the application and add the courses by semester for each school. If you got transfer credits you’ll include those. You quite literally write exactly what’s written on each transcript.