In third round there are vacancies in elite colleges,this is because many students get allotted in csab (now josaa) in 2-3 rounds and most of top 1000 rankers prefer NIT/IIT .Also even upto rank 1500 many of them prefer NIT/IIT's just for tag!
In 2014,there were approx. On average 20-25 seats vacant in COEP,VJTI,PICT that too cs,entc,etc for 3rd round.
But with 95 percentile you better can expect PICT and not COEP/VJTI, even plain electronics in VJTI in 3rd round.
Process-They create time slots according to SGMs,when u enter hall at ARC(counselling i.e 3 round is conducted at one of the ARCs according to regions) you have given a pc,login in your account,add options. Then a live screen displays the allotment according to SGMs.

All the best !