Will I have to create course every time when I add semester?

No. You need not add course each time. Once you add a course, you have to add batches inside it as and when needed. Students will be admitted to that batch in that course. 

Suppose if the course is BSc Physics.

Course: BSc Physics

Section: Sem 1

Batch : Jan 2013

Now the next batch of students in Sem 1 BSc Physics may be in June or Dec.

So you can create  a batch under the course BSc Physics

Course: BSc Physics

Section: Sem 1

Batch: June 2013, Dec 2013.

So you can go on creating the batches inside the Course.