The only thing you can do is amend.
There wasn't any change in 2014 in this regard (but there was a clarification for disposed property in 2007, and the Revenue Procedures were revised in 2015).
Although Form 3115 can be used to 'catch up' on the missed depreciation, one requirement is the you must used an "Impermissible Method of Accounting". I've seen some people assert otherwise, but the Revenue Procedures clearly say it "applies to a taxpayer that is changing from an impermissible method of accounting for depreciation to a permissible method of
accounting for depreciation". Although not claiming ANY depreciation is "impermissible", claiming the wrong amount is not "impermissible" (it is a "mathematical or posting error").
As for the software, you should put what you SHOULD have taken.
It is an option in the software because if your business percentage varied over the years, TurboTax does not keep track of that, so you would need to enter the proper amount (otherwise TurboTax assuming the current year's business percentage has always been used).
Yes, you need to enter the full amount of depreciation you COULD have claimed. In the event the property qualifies for the 2-out-of-5 year exclusion for using it as your Main home, there is an interesting exception (sort of) that TurboTax doesn't handle. In the event that applies, please post back with details about when it was your Main Home.
