We also didn’t charge them rent while they were in temporary housing.

If there is a shortage of housing you can charge more rent.

So does anyone else have a situation where there are other fees that are charged when a guest arrives (e.g. parking in the building, etc.).  

And if I feel the flooring is in good condition, even if not new, when I’ve had applicants that didn’t like flooring color (usually use a darker taupe), I tell them that’s what area rugs are for.

Vacancy charges, repair charges, what are all the fee's.

I would also charge a lot more than I would for a residential rental.Honestly, I wouldn't recommend it unless you've really studied it and understand how to protect yourself and earn fair compensation.

Main attraction was flat rate management fees vs % that everyone else charges.

I'm about to rent out my first property and would love a recommendation on an app to use to screen applicants, submit maintenance requests, and receive rent. 

I have two applications from the same household.

Can I charge him my late charge which is currently $100 after I get the rent on the 19th?