I've issued separate checks for labor and materials, for my bookkeeping convenience, though you can separate the expense items on the check remittance advice.Just to say if you're gung-ho on doing the 1099, just do it, you don't need time logs justifying it.

And those will require a bookkeeping program such as QuickBooks.

But your post asks more so for a bookkeeping / accounting software. 

I changed jobs to get a promotion and more pay, my wife took on a W2 job, we pivoted my wife's Coaching business to a Coaching and Bookkeeping business; adding a couple clients right away, and we purchased a Candle Business with Seller Financing and a low amount of money down.

At this point I'm guessing that's fine and you just want to get your closing done (can't blame you, I'd do the same).Worst case scenario, you catch up on your bookkeeping for this year and mock up a Federal and State return (pretty sure RI only cares about the state but they might want both), using good faith best-guess numbers, with PRO FORMA written in all caps at the top of the first page.But it would be much better (and faster) to pay a CPA to do it for you.

.-50 units and under-paperless system to accept application, screen tenants, background checks, sign documents/leases, accept rent payments, auto reminder to tenants, accounting/bookkeeping software, produce basic financial reports, and auto post to craigslist/etc.

So I created an expense account report that I file for rental expenses I paid, same format as I used at the company, reimbursed myself from the rental checking account, and the expense categories corresponds to the Schedule E expense categories, so when I prepare my expense report to myself and pay myself, I handled banking and bookkeeping at the same time.

In our last conversation, my builder friend mentioned the biggest value add was his great bookkeeper.  

@Melissa Matthews I found rei bookkeeping.

I am going to bring my books up to date and get a referral from my accountant for a bookkeeper locally to set my Quickbooks up more Real Estate/Accountant friendly as far as categories go and have this bookkeeper prepare the year end reports for my accountant or teach me better how to use the program so I can do it.