Well I have been using quickbooks for years. But I don't utilize all that it's capable of doing. My accountant likes it and it's easy enough for me to do basic things like have two or more buildings with different checking accounts and mortgages in one program. I'm not much of a computer person but I use excel in the most basic way to cross check what I've input to quickbooks and so there's no confusion later about who's rent was deposited, who paid cash ect. I just keep a simple chart with each building, the list of tenants, how they paid, when they paid, when it was deposited and how it was deposited. In other words if I deposit through my phone app I record that I've done it that way. I only have twenty units but I have found it can be very easy to miss something especially when some tenants pay cash and also many tenants pay the same amount as others.
It would be great if everyone paid the same way and exactly on the first of the month but it will never happen that way.
Also I use the "Evaluator" app by real estate tools.com.
I find this invaluable as far as tracking expenses, changing expenses, changing rent amounts, interest rates ect to see where we are going and also to evaluate a potential buy.