With multiple entry visa, you have to leave Thailand within the entry stamp of 90days. You can apply for a 1-year extension anytime (but only when your stamp has
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days or less, depending on your immigration office), on your first entry stamp, the last stamp, or any from your visa. Totally up to you when you want to apply for a 1-year extension.
Your extension continuity was terminated when you left Thailand without a re-entry permit. For PR, you are going to start over. Your count will start when you get a 1-year extension again.
(PR is out of the scope of this group, so don't go further)