So if you lived there for 3 years, they shouldn’t charge you.

You definitely don't want a situation where someone gets hurt by traps or poison that you place.If it is more related to the tenants being pigs than a hole on the outside then it may require some education on how to keep things clean and charging them for pest control if local law allows it etc.

So my question is how can I protect myself if I do take charge of the apartment in the back.

I actually have no way of knowing for sure if he has gotten any of my communication, so there really couldn't be any kind of harassment charge.

Charge more for the rent back and have escrow withhold some money as @Andrew Boettcher suggested. 

What rents are they charging?

But they dont tell you that realtors will charge 10k for the 150k house, closing costs, holding costs on the buy and the sell.

I’m curious about your experience renting. you can...i basically just found a really responsible relative and convinced them to move into our upstairs apartment for the same rent they were paying at their old place. twice the size and much more beautiful. we figured it was best to charge less than market rent and have peace of mind with someone we knew to be responsible than to try to charge market rate and play russian roulette with tenants in the Bronx. 

To name few features, you can connect your bank & credit card account(s) to QBO to automatically download the transactions daily, set up rules for any recurring charges, setup recurring transactions (ie invoices to tenants), sent out reminder (individual or batch), accept online payments (cc & bank) which can be tenant or landlord initiated, track multiple income sources (ie. flip, rental, wholesale), track individual properties, charge tenants for reimbursable expenses, track 1099 contractors (and e-file tax forms), and create a budget.

Does Ypsi really charge separate taxes for each side.?