MFJ usually saves money, but it makes you each legally liable for any errors, omissions or misstatements on the joint return. I'm surprised your attorney would advise this--hopefully your spouse is honest and truthful on their tax information, and you are honest and truthful to them. If there are any shenanigans suspected, you should file MFS even if you may pay higher taxes.
Anyway, yes, as stated, if your spouse already filed MFS and you did not file, the correct way to file MFJ is for your spouse to file an amended return and add your information. You file nothing separately. The fact that you filed an extension under the assumption that you would later file MFS is not an issue.
Note that if there is a refund expected from the amended joint return, the IRS will not do direct deposits on amended returns, they only mail paper checks, to the address used on the return. You should have an agreement about how this will be divided. And the amended return will probably take 4-6 months to process.
