Please note that I am strictly talking about software for book keeping purposes.I only know of Quickbooks and Sage

Do you just provide your book keeper/accountant the HUD1 or do the feds issue 1099 from info the title co provides them?

First thing I'm going to say is that their bookkeeper sucks. 

I don't have a ton of experience, although I have managed our 2 units for a year and a half now, handling leases, bookkeeping, open houses, etc. 

the safe harbor applies to amounts paid during the tax year to acquire or produce what the regs call a “unit of property” (UOP), you must meet these requirements: (1)you need to have written accounting procedures treating as an expense for non-tax purposes amounts paid for property costing less than a specified dollar amount (which will be 2500 for you), or with an economic useful life of 12 months or less;.(2) the taxpayer treats the amount paid for the property as an expense on its books and records in accordance with its accounting procedures. ( do this on your bookkeeping software or whatever you utilize)(3) the amount paid for the UOP doesn't exceed $2,500. as substantiated by the invoiceNote: The cost for the Unit of Property includes l additional costs (for example, delivery fees, installation services, or similar costs) if these additional costs are included on the same invoice with the property. 2) Small taxpayer safe harbor: To be eligible for the safe harbor, the total amount of improvements for the property for the tax year may not exceed the lesser of $10,000 or  2% of the property's unadjusted basis. 

Especially if you keep a bookkeeping system where all expenses, including this one, are recorded.That said, if you do have to prove this expense to the IRS, you have to prove two parts.1.

I tried to cheap out on managing my own properties, my own book keeping..

These are good scores, great in my book. Keep

For each line item, use a cost code as well so you can track how much you are spending from project to project and make the book keeper's life a little easier.BANKIf you are using a construction lender which is likely, make sure you get permission from the bank that it is ok to do grading and demolition before the loan is originated. 

I found a QB bookkeeper that was instrumental in helping me get it set up correctly.