As
@El***
correctly stated you can apply for a yearly extension when you have 45 days or less left on your current entry stamp (the validity of your VISA sticker has nothing at all to do with you applying for an extension because a visa doesn't let you stay IN thailand, it lets you ask to get in and it's the small blue rectangular entry stamp you got when you entered using that visa that actually lets you stay here)
Seeing as your 90 day entry stamp expired MONTHS ago, and you're on amnesty you can apply for a yearly extension anytime from now until the 26th of Sept <- the day the amnesty you're on now expires.