Can I apply for a marriage extension in Thailand with monthly bank deposits?

You definitely need to check with your specific immigration office as far as if they will allow monthly income by transfers for yearly extensions based on marriage.

More than a few people found out the hard way their office wouldn't allow it and they needed to bank the 400K baht for 2 months to get the year extension.

The requirement is 40K baht a month, not a baht less, each month, every month for the previous 12 months, you need to make sure at least 40K baht gets in to the thai bank account in your name only every month from international transfers <- and that's IF your immigration office will allow it

You're comin' in beginning of next year on a year long, multi-entry Non-O visa that will give you 90 days each stamp, and you'll bounce out and back every 90 days for the year (as that's how that visa works), so you have plenty of time to get to your office and ask if you can do the monthly transfer method for marriage extension.