Him and his wife worked 3 days a week and they only needed 1 part-time bookkeeper and 1 part-time handyman to manage a portfolio of 100-150 rent to own single family homes.

Due to improper bookkeeping. 

I have not yet finished the  Bigger Pockets book on real estate investing, and am reading some other sources—- I’m just looking for some general conceptual pointers about how the book-keeping acutallly works.

From hiring, firing, payroll, to daily book keeping, I've done it all. 

Also, I'm a CPA, so luckily I can do my own taxes and don't have to worry about bookkeeping costs.

It might help to get a good bookkeeper separate from your CPA. 

These safe harbor rules contain capital account bookkeeping guidelines that establish uniform procedures for recording the economic (not tax) results of partnership operations.

Have you considered using a RE bookkeeper?

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) at the beginning of the tax year, the taxpayer has 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 invoice.Note: The cost for the Unit of Property includes additional costs (for example, delivery fees, installation services, or similar costs) if these additional costs are included on the same invoice with the tangible property.Eg:A purchases 100 printers at $500 each for a total cost of $500,000 as indicated by the invoice.

I am looking to get advice on tax reporting and book keeping, I do have some accounting knowledge already but would like to learn more.