How are you uploading your new users? You can upload them via a csv file/excel file and they will be on your Moodle - you then enrol them manually into the courses you want them in or else get them to enrol themselves (might be quicker) As you have discovered if you enrol them via siteadmin or category they will be students in every course (or every course in that particular category) You can actually enrol them into courses (if they have been made already) as you upload new users if you have a look here: http://docs.moodle.org/en/Upload_users#Upload_file_format
Roles and permissions
Student Role Question
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