How can I choose which student is in which group?

You can assign students to groups in "Students" window:

Select class on the right side, then select several students (with Shift+click or Ctrl+click), right click in corresponding column and select group for these students.

Notes:
- This dialog us useful e.g. if you want to print individual timetable for each student.
- Information from this window is used also in Electronic Class Register.
- You can not combine groups from different divisions on the same place in the timetable, even if these groups have different students selected in this window. If you need this, you will have to use Seminars instead of Groups/Divisions.