Do I need to leave Thailand every three months with a Non-O spouse visa or can I get my passport stamped at the local Immigration Office?

If you don't want to border, bounce like that for the validity of the visa, when you have 30 days or less left on any of the 90 day entries from that visa you go to the immigration office with documentation and proof of funds (400K baht banked in a thai bank account in your name for 2 months prior to your application OR a notarized letter from your consulate stating you get over 40K baht a month in income from abroad) and apply for a "yearly extension of stay" for 1900baht. It will go under consideration for 30 days then you go back and get the year extension inked into your passport.

Once you have that you no longer need to leave thailand every 90 days and instead you would do 90 day reporting at the immigration office.