We do not have any joint accounts and he has no association with the LLC, but I still don’t trust she couldn’t come after me.My concern is that since he and I do not own a primary residence, which an LLC is designed to protect, the duplex as my main asset and source of monthly income would be at risk. 

Learn about landlord insurance, umbrella insurance and renters insurance.As to checking accounts, a personal account would do, a joint one if you have a partner.

This might cause you a legal head ache.2.

I'm just trying to find out what the benefits are for someone if they sell their house as a short sale and then file their bankruptcy, as opposed to not doing the sale and just doing a ch. 7?

The tax benefits can be enormous for couples filing jointly where one is a high wage earner and the other has time to focus on real estate.

And when rent is late, I only accept the full payment (rent+late fees) and only in certified funds (money order, cashiers check, cash, ACH) because I don't want to spend another week waiting for a check to clear (or bounce).You are creating additional confusion with your "$5 per day" late fee.

Do Joint access per every two lots. 

or is it a joint venture with other investors?

I have signed many times as a co-guarantor (the words "jointly & severally" still make me sweat) on a multi-million dollar commercial or construction loan, where I only had fraction of the ownership interest.

After my own reasearch I choose to go with tenant cloud and pay for there upgraded package to accept ACH payments with no fees and list to other platforms for vacancy’s.