Did you code all the income correctly and enter the correct amount for border city exemption for each spouse?  If so, you should see the respective amounts reported under each spouse's column on AR1000NR and AR1000ADJ.

So long as AR1000NR is correct, AR3 will ratably allocate the correct amount of I/D to each spouse based on their AR AGI (see Lines 31 to 35).

Here's a screenshot from a dummy return with border city exemptions and I/D reported to each spouse: