I would first suggest you do chat with support. They can look at the file and help you get things in the correct spot. I find that the software generally gets you the best results when you enter the sale through the dispositions screen. 

If you could list a generic version of what you are starting with, that would help. e.g. Selling Improved Real Estate for 1,000,000 - There are 6 assets = Building, Land, New Roof, HVAC, Paving, Remodel - All assets are prior year assets,....