The 50% allocation is between a rental Schedule E and personal deduction Schedule A for taxes and interest, not between two rental properties.[you will have to calculate the allocate of interest,property taxes and insurance to each when they both become rental units]
You can wait until 2017 to change , I misread the conversion as in 2016.
You will not confuse the program.
Generally unless you are really fortunate both units are not always rented at the same time and the same number of days.
Proceeds and selling expenses are allocated 50% to each a rental rental and personal side that will still be in 121 exclusion time frame when sold.
Personally break down quadplex to single dwelling for tax reporting and do any allocation before hand to enter into Turbotax.
When you have the desktop you can save your tax return with a unit test name and do a run through before the taxes are due next year.
