I read the fees page, but they have different fees for invoices by e-mail, online payments, and mobile app payments.

Find a management company (LeParulo was decent, and I haven't heard otherwise lately...) that invoices you, and doesn't have in house maintenance.

If he owes enough you can likely go to eviction after the initial notice but it might be best to clearly invoice the rent and late fees and start with pay or quit notices per your local laws. 

We have our bank account set up where we can accept payments from PayPal, Square or send them an invoice through our bank account or web site or square.

So now we are typing up a certified letter to send to them about the policies outlined in the lease that they have agreed to and are in violation of as well as an invoice of money owed as they will not return our calls.

One of the issues we're having is how to input rental income, property management fees, etc without having to create an invoice or bill for them every month and then go back to show it paid. 

Is the cash withdrawal showing up in my bank account enough proof or do I need some kind of receipt or invoice from the person I'm paying?

@Dawn Anastasi - Besides the lease, 5 day, and copies of communication and extermination invoices, anything else I need?

There was no estimate, only an invoice.

We provided the quote and uploaded the vendors invoice (which you will see on your statement when the bill post this week) and per your PM agreement, added the maintenance charge on your rental statement.