First you need to fill up a small form which asks your rank and other details.
Then the next your 10th and 10+2 certificates are verified.
Then next stage is selecting the branch where the students are called one by one in order of their ranks and are asked to opt a branch and the first year fees is also paid at this stage. If the preferred branch is not available, then he/she has the option of applying for wait list for that branch and opt for a different branch.
If the student only opts for wait list option then they have an option of pay the fees later (not perfectly sure about this step).
The counselling takes place in all centres of Manipal university in the country and live status of the number of seats left in each branch is shown at the centre. There are small brochures available at the centre which have information about every department and branch.