Your 90-day time period will not be calculated from your current permission-to-stay date; rather, it'll be calculated somewhere between your application date and the next 4-7 days. At least that's the way it's done here in Chiangmai. I realize you're in Bangkok and, as DrJack says, you need to apply at least 15 days prior to your current permission-to-stay date (whereas, here in Chiangmai, it's at least 21 days prior).