@Sof ******
first time I've come across an employer acting like that, my employer did all the leg work for my wife and she just had to turn up to immigration to have her photo taken.
If you haven't already then best place to ask is in the Thai Visa Advice group, although the mods are also in here so I'm sure they'll help if they haven't done so already :)
If you do ask on there then, just to be clear on what you want, ask for how to go about getting your extension of stay as a trailing spouse and that you're currently still on the 3 month visa itself.