Or are you underthinking it?  The first step is to consider the whole building.  You paid $100,000 for it and you figure the land is worth $10,000.  From there, allocate the $90,000 but don't say upstairs residential is worth the same as downstairs commercial.  Are they all the same square footage?  Is there an elevator?  (Maybe use component depreciation here.)  Could very well be that each downstairs unit is worth $35,000 (how much rent do they earn?) and upstairs only $20,000.

In other word, don't start by dividing the building into pieces and then put it back together.  Determine the value of the building, then allocate its parts.  Your software might ask for the value of the land, but IRS doesn't ask until the place is sold, or the Schedule E is audited.  

Interesting question would be, what if it's turned into a condo?