This is a bit complicated.
For the years when you were married but your spouse was a non-resident, you have two choices.
1. File as married filing separately. Only report your income. If your spouse does not have a tax number, leave it blank and write "NRA" in the space for their tax number.
2. File as married filing jointly. To do this, you must make a choice to treat your spouse as a US resident for tax purposes. This means that you must report and pay US tax on all their world-wide income. If they also pay tax overseas, they can claim a deduction or credit which should at least partially offset the foreign taxes.
You were never allowed to file as single. You must amend to either MFS or MFJ. MFS usually has higher taxes, because some deductions and credits are limited or reduced, but that needs to be balanced against the possibility of your spouse's overseas income being taxed. How much more or less tax you would pay by treating your wife as a resident and filing MFJ is something you need to test for yourself.
Your wife is a "US resident" for tax purposes for any year that she has a green card, plus any year that she is living in the US and passes the substantial presence test, even if her green card was not approved.
https://www.irs.gov/individuals/international-taxpayers/substantial-presence-test
For the years your wife was a US resident, your choices are
1. File as married filing separately. Each spouse must file a separate tax return that reports their world-wide income.
2. File as married filing jointly.
