The official Website holds every answer to your question.

1. The first step is certificates verification. The list of certificates to be verified will be put up in the website and a centre and time is alloted as per your rank.
2. After your verification of certificates is done,a set of dates are alloted for putting up your options for desired college and desired stream. Based on this,you will be alloted a seat in a college .
3. You need to download the allotment order from the website and a challan will be generated (from the website only) and you have to pay the fee for entire year then in a bank.
4. Again there will be a call​ for second round of counselling (putting up options).
5. Again you will be alloted a college based on your options.
6. You need to submit all original certificates (verified during step 1)and submit them in your college before a specific date.
7. You will be generating Challan again with allotment order.
8. If the college alloted in the second counselling has fee more than that of the first alloted college,the Challan will be generated for the balance amount. If the fee is less the remaining fee will be refunded.

Everything will be clear if you keep referring to the official Website.

Hope I am clear.

PS: No Challan will be generated for the students availing fee reimbursement from the government.