I'm not really "up to snuff" on state taxes all that much, because my state does not tax personal income and never has. But if you sold property in NC at a gain, you'll report it on both NC and CA returns, and you will pay taxes on that gain to NC. The CA tax on that specific gain "might" be reduced, if CA has a reciprocal tax agreement of some sort with NC. I don't know if they do or not.
Finally, when dealing with multiple state tax returns, do the resident state return *LAST*. Otherwise, if any reciprocal tax agreements exists between any of the states you're filing for, those agreements can not be "taken into account" by the program.
For long term residential rental property, it is not common to show a profit on SCH E. Especially if there's a mortgage on the property. It's more common to actually show ever increasing losses with each passing year the property is rented. Typically, there is no taxable gain until the year you sell the property; and only if you actually sell at a gain.
