If our agent pays him via checks and bills us at closing, does this have any +ve or -ve impact on the taxes? 

And we pay them direct from rehab draws on my loans.6.

Hard work, preparation, proper setup and service goes a long way to assure a bright future.

The difference is that on the 2k house you can pay for that HVAC relatively quickly, where as the 800 house it takes many months to offset the costs.The same can be said for other costs such as property management. 

Not sure if it is worth it to just pay them out or proceed with evictions. 

When we were the lender we would foreclose on the property or have the HOA buyer pay us off.

The SFH and the 1b/1ba ADU are currently occupied by tenants under RSO and paying far below market rents.

Even though I was cash challenged I held onto my house (putting past due payments on the backend) and had equity to sell, pay off debts, and get my credit in check.

I would absolutely understand how to properly thread this needle with the help of a good CPA. 

I dont think you need advice for anyone how to structure this your already experienced operator.. the decisions is do you want to keep adding doors or concentrate on paying off what you have.