Hi, 

If you are referring to the aiq counselling then theres no need to fill different. Once you have registered for counselling and paid the fees you can fill choices for both bds as well as mbbs. 

If you have paid for only aiq then you cannot apply for deemed universities. However if you have paid the fees for deemed universities you can apply for both aiq as well as deemed university counselling. 

You nees to fill the colleges as per course from the list of colleges provided at the tike of choice filling. All the bds and mbbs colleges are present together from where you need to select your choice of college and fill the options.

But be careful while choice filling since it does play a vital role in counselling process

All the best