Just keep reading, listen to the podcasts if you haven't started already(SO motivating and filled with a wealth of applicable information) thanks @Joshua Dorkin and @Brandon Turner.

I have a few questions:1) What accounting software would allow me to maintain multiple properties and allow me to invoice my tenants for rent, utilities, repairs, etc?

I suspect that this will give me more applications so I can select the best tenants.

But with the hard money lenders, they're just going to ask you to submit a loan application and an itemized list of the repairs.

Do you have a formal application and screening process developed?

I got it off HUD auction and it has too many use restrictions for any lender to lend on it; and buyer's loan application is getting rejected from many places.

If your employer's payroll software is not designed to compute withholding amounts for more than 10 allowances, it will probably just withhold for 10 even if you claimed more allowances. 

Also Application fees?

I dont have personal experience with either, but I have tried to protect myself from both.My application has a spot on it where they are required to list an emergency contact person who can assist in their move-out if they become deceased, hospitalized (long-term), or incarcerated.  

With many software companies specializing in web based with log ins for owners there is no reason you should have access to your own cash flow reports when you want-units:staff ratio.