I love the AirBNB model, I don't want money showing up in my bank account until the guest is staying - advance payments make bookkeeping really difficult (I don't want a bunch of $ coming in in Feb-March for summer reservations, then very little over summer months when the properties are actually making top dollar!)

Invoicing electronically throughout the whole bill, receive payment, deposit and reconcile cycle can ease the bookkeeping burden.

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?