HMM;  entering the data your way is very unnatural for  accounting.Expenses & Invoices are unique accounting events and QB does that well.I understand your desire to correlate transactions - - that QB does poorly. 

Consumers see mold, scratched floors, and chipped paint; investors see invoices and rent checks. 

Do this in writing by sending him an invoice or letter that states you are doing so.

so I requested an invoice from the actual contractor that did the work.

Intuit also offers "Intuit Payment network" which charges 50 cent transaction fees for ACH transfers and invoicing feature, recurring payments etc. but it doesnt seem to have the same level of unit tracking or auto reminders that sparkrent offers.

Are they keeping copies of all invoices throughout the year in case of an audit? 

The invoice from a PM should be clear as day.  

Why pay the overhead to a PM company to essentially mark-up invoices and pass them along to you?

Remotely log into it from any computer/tablet/phone and I have access to my excel files, pics, invoices (PDF), leases (PDF).

I have been using Quicken's Rental Property Manager since my 4 properties are basically pass through but its not the ideal because you have to rig it up a little depending on if you are using invoices and with the use of tags you can differentiate between properties.