@Raki *******
you apply for the extension before your 90 day stamp runs out (you can apply any time you have 30 days or less left on your current stamp) you will pay the 1900baht and you will get an under consideration stamp (in bangkok it's for 3 weeks now but most offices it's for 30 days) then you go back on that date and get the year extension inked in.
IF you need to travel after you've applied for the year extension and are on the under consideration stamp you MUST buy a re-entry permit (and it will be valid only for that u/c stamp)