Depreciation per unit vs square footage tax implications

[Peter Morgan]

Hello,

I wish to know what are some best practices to depreciate an owner occupied two unit property is it by square footage or per unit? More often than not the square footage of the each of the units of a two family home can be significantly different. For example the unit owner occupied is 2/3 rd of the total square footage while the rented portion could be 1/3 rd of the total square footage.

In such situations would it make more sense to depreciate by square footage to optimize tax?

What if the CPA goofed up and depreciated per unit over few years is there a recourse to this? The reason I ask is when selling such owner occupied units 1/2 of the capital gains will be taxed instead of 1/3rd.

I will greatly appreciate your inputs.

Thanks