I submitted a return separate from my wife, but we now want to file jointly. I know I need to file an amended return, but what does she do since she has not filed yet?

She will have to wait for your return to be fully processed and then you amend the separate return to switch to filing jointly.   She cannot file a joint return at this time----it would just be rejected.   

Right but in the meantime until my return is fully processed and I can submit an amended return does she need to do anything? If she doesn't file by the deadline won't she get hit with late fees?

No she doesn’t file her own return.  You just amend your return to Joint and add her info to it.  

If you are getting a refund on the joint return there are no penalties or late fees for filing after the deadline.

Oh--and let's review----you are the one who went ahead and filed a separate return, thereby precluding the filing of a timely joint return.....but you are concerned that "she" might get hit with a penalty?   Not how it works Mr. Husband.....the penalty would be shared and would really be your fault.   But....if there is a refund on the joint return, there is no penalty.

Very much appreciate the answers and the information, thank you! If you're ever looking for help off that high horse I would love to repay the favor! 🙂 

I would suggest she file an extension.  Not sure why no one else thinks it is a good idea.