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.

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?

Motivation is an emotional response to a circumstance, not the circumstance itself.Here’s the bottom line:You can’t target motivated sellers.

I like that you can setup different virtual accounts for security deposit let's say, or to separately ledger cash collected through a rent to own contract.

we just managed to get ong to run all new lines and separate meters for our whole apartment complex at no cost to us. 

Question 2: Is it a good idea to put every piece of property into a separate LLC entity (1 for 1) or is it okay to put a few properties into the same LLC?

If it is a pet, be aware that they could get paperwork saying it is an emotional support animal (if so tell them it needs to be from a local medical professional not a website) or say that they don't have a pet.

For separate entities I use separate files for each entity.

You can simply request a separate check for the $100 increase to bring the total deposit in line with the new rent amount.