First time has to report in person. It's better to fix an online appointment/ booking to avoid hours long qué. Onwards next until your visa is expired or leave Thailand, you can submit your report online and it's very simple. It's useless to pay an agent.
, you are inconsistent with your statement. I quote you. " Yes it's a hassle, I'm doing that right now and is finally on the last step to go to the local district office to register my marriage" . So, I thought it's your first time. You also stated that you are permanently living in Thailand since 16 years. So, why are you going through the process again? However, I am not an Indian and have been living in Thailand for 6 years. Thank you.
It's a very lengthy and complicated process brother! You have to translate your Indian marriage certificate in English and then attested by the concerned authority of India (maybe foreign Ministry and law Ministry). This certificate you have to submit to the Thai Embassy in India for attestation again. That attested certificate again you have to translate in Thai language after you arrived in Bangkok and again have to be attested by the Ministry of foreign affairs, Thailand. Again you have to submit the attested certificate to the concerned district office, Thailand to get the final marriage certificate in Thai language. Please inbox me if you need further cooperation.