Amending return to file jointly, but only one has filed so far.

Hello! My wife and I got married last year and it's our first year filing taxes as a married couple. We (I) thought it would be a good idea to file married but separate to possibly maximize our return, but didn't know about the Roth IRA penalties that come with that option. We filed her return first, and found out about the penalties while I was working on filing mine. I still have yet to file. Here is what I am wondering:

Do I need to go ahead and file my return as separate, and amend afterwards?

Or can I file her amendment and have that count as my return as well ?

Or do I file mine as though it were jointly and her amendment at the same time?

Also, she received money back, and, if I filed separate, I would've owed around $800 in federal. If we would've filed jointly, we would only owe a little over $150. I assume that any payment corrections would be handled by the IRS and they'd send us the proper documentation to inform us of this. I just want to make sure I don't cripple my family's future or anger Uncle Sam.

Any help would be immensely appreciated!!