What I would do is try both and separate the leads from each and see which one is better.

One workaround could be keeping a separate spreadsheet to track your adjusted tax basis accurately and only using Stessa for operational insights.You could also reach out to a cpa and see if they have a specific recommendation for software to use.  

What is the best way that you have found to tell them that you need labor & materials separate, so at tax time you can send them a 1099 for labor?

Two separate property appraisers (at the direction of the lender) were sent out to appraise, and neither was willing to appraise it as a "residence", and thus financing fell through (conventional primary loan).

Another idea could be to see if the HVAC system can be adjusted or modified to better separate the airflow between the units.

You will receive the security deposit in Checking but then transfer it to Savings.Savings: Hold the deposit here so it's separate from operating funds.

I would suggest doing these separately however since you will run into issues with a partial release clause on a blanket loan.

Utilities are OFTEN overlooked so reach out to power, telecom, gas (or go all electric), water, and sewer to make sure you understand what it would take to get separately metered services from the primary house.

Separately, the benefits and disadvantages of renting to Section 8 is a topic of extended debate on this forum.

The property does have heated radiators through out each unit. everything is separated for each unit electricity, gas, and window units in each property.