I want to take admission in Pvt MBBS courses in South India with 540 marks

Amit, you haven't mentioned the State and Category you belong to. This is important because Private Medical Colleges do not participate in All India Counselling and the seats are filled through State Counselling alone. And for appearing for State Counselling you need to hold the domicile of that particular State. Or else the only other option is through Management Quota. Under All India Quota, All the 15% of All India Quota Seats except for Jammu and Kashmir, 100% Seats at Deemed and Central Universities, IP Quota seats in ESIC Colleges, Seats at AFMC are filled by DGHS. The 85% State Quota and Private Colleges are filled by the respective State Authorities. And there are 3 Categories in Private Medical Colleges. Category A is the Government Quota Seats. And only candidates of the home State are eligible to apply for these seats. B Category seats are also called Management Quota Seats and they are filled through  State Counselling and the remaining seats are filled through direct Admissions by contacting the College directly. Here the fees is usually nothing less than 40 lakhs. The last Category is NRI seats Category and you cannot apply for that.
And having said all this, you can apply for Karnataka State Counselling because Karnataka is an Open State. Sonwith a score of 540, you can appear for Karnataka State Counselling and secure a seat in one of their Private Medical Colleges. The rest of the States, you cannot participate in their State Counselling which means Direct admission is the only way. This is not just for South India but across India.