I figured it out! In case anyone else runs into this...
Do NOT choose to "Allocate earnings using form IT-203A Zone 1/2".
Instead, choose "Allocate using another method"! (The "Learn More" info is not clear.)
Doing this, you will be able to simply enter the amount of your earnings for Zone 1 and Zone 2! It will then ask if you made any estimated payments; enter dates and amounts.
When you finish, it'll ask about the spouse. If you enter an amount under the threshold, it'll tell you there's no tax due.
Apparently if you are part year resident or non-resident of NY, choose to use IT-203A.
