All state tax returns use the federal tax return as a starting point for calculating state taxes. It doesn't make any difference whether you are filing part-year, full-year or non-resident state returns - you have to start every state return with whatever is reported on your federal return.
If there is income on your federal return (e.g. capital gains or losses) that does not apply to a particular state return (e.g. a non-resident return), you will have to make an adjustment (allocation) in that state's tax interview to keep it from being taxed. Even if it is not subject to tax by your non-resident state, you still have to start by reporting it on that state's return.
