I have alloted a college in first phase counseling of ts pgecet and i paid the fee and i want to go for second counseling so do i need to pay again online certificates verification fee and do i need to apply for the certificate verification.

Yes. Obviously you need to pay the fee. If you have just paid counseling fee in round of of counseling then that's for your purpose. But if you have paid College fees then do ask for refund in the College if you don't want the alloted seat.

You need no register again. Registration is one time process. You just need to apply again in the next round in the Colleges you want by paying counselling fees.