For example if you did a bunch of reno work and rather than putting it in line 14 lumped together you put in line 19 with a "see statement 1" and then statement 1 has itemized reno costs that match invoices you can share with me dollar for dollar and line by line (force your CPA to do this, she or he will not want to... and obviously keep your invoices that your contractors provide!)

There are several ways you can arrive at the exact same number; I've found the quickest is to take gross rent, subtract recurring non-PITI expenses, divide the resulting number by 12, and subtract actual PITI from that.If you want to argue that something is a non-recurring expense that you shouldn't be hit with, like a massive electrical upgrade, be ready with receipts and invoices. 

John Smith is licensed to do HVAC work with a dba to The-AC-Corp, you call The-AC-Corp and you get an estimate from James Miller and he does all the work and bills you under the The-AC-Corp with his name on the invoice.

You can add your bank info to hemlane and once you get invoiced hemlane pays from that account.

I have not used it yet, but am looking for a service to schedule invoices and send them to their email.Or here is a huge list of online invoicing services...http://smallbusinessbonfire.com/send-online-invoices

We use Quickbooks to manage some of our internal tasks like expense tracking, invoicing, etc. but Use bench to manage all of the more tedious tasks like bank recs. and tax prep.