I agree with the comments above, QuickBooks Online and using classes is the way to go. It allows you to line up your income statements for each property and compare each expense account to all other properties. That helps highlight your problem areas.
For my properties, I go one step further and add a short description to each transaction. It is especially useful for tracking repairs and maintenance as you can drill down for any period of time and get a quick report of everything that has been done (... didn't they just repair that shower in 2nd bath at 123 Main Street last year or was that Easy Street?).
One last benefit is if you have multiple property management companies in different cities providing reports in various formats it can be difficult to compare your investments with each other. By entering everything into QuickBooks you can bring all the square and round pegs together in one clean format.
QuickBooks does have a learning curve to it, but I cannot imagine how you keep track of your portfolio without it.