My son was a resident part year in Alabama, then moved to Missouri. His job is online but headquartered in Alabama. Turbo Tax is saying he has to fill out both a 40R and 40NR for Alabama. How does he go about that? Does he split the deduction percentage wise? He's filing single.
This situation is called "part year resident". Your son would need to file the form 40R to cover all the income while resident in Alabama, and the form 40NR to cover all the income sourced in Alabama while non-resident.
A nonresident taxpayer who receives income from Alabama sources or for performing services within Alabama and who also had income while a resident of Alabama during the same tax year must file both the Alabama Nonresident Form 40NR and the Alabama Part-Year/Full-Year Resident Form 40.
If you are required to file both returns, the total personal exemption ($1,500 or $3,000) and the dependent exemption ($300) must be claimed on the part year return (Form 40). No personal exemption or dependent exemption can then be claimed on the nonresident return (Form 40NR).
For non-resident period, income from Alabama sources when concerning compensation for work is income paid for work done while being physically present in Alabama. It doesn't matter where the employer is, what matters is where the employee, your son, is.