Hi all, thanks for the comments for my last post. I couldn't reply back because comments were turned off.
Anyways I went today to hua hin immigration, and did my 30 day extension, on my tourist visa exemption stamp. I had no problems with that at all. I tired to ask them if I could do my extension after the free amnesty and I didn't get a clear answer.
So as James Miller suggested, if you can do an extension it would seem be safer to do it. Thanks again for all the advice. All the best.