Always use a single upload file. Always use this file to add new students to the *.csv file and set the upload parameters to whatever you need in the "Upload users Preview Page." I know it is not clear, but if you read the documentation on uploading users, it should become clearer. Just be careful about how you set your uploads and it should work for you.
Things to remember about user upload files. You can delete users as well as add users. Add a column headed '...,delete,...' in your csv file, matching the field in the main user table, It should contain either a value of 0 for active or 1 for delete, so you can bulk delete users as well as bulk upload. You should have a dump of your database somewhere so you can remove all deleted users in bulk once a year with a DELETE sql statement, as long as you have that backup. You will need to trace all records of that user and delete them with a rather large statement with lots of inner joins I would think. You can add in the classes students should be enrolled in, the cohorts or groups, but I have found this a little tiresome, trying to administer it. Best keep it simple, let Teachers and Managers add students to their classes, or Cohorts or Groups.