This isn't a question about which software to use, or how to setup Quickbooks. I'm committed to trying Quickbooks Pro Desktop for Windows to handle the books for a 12-unit property I just closed on. I have a specific question about entering transactions. I'm investing out of state and have a property manager that uses App Folio, so I'm not planning on using Quickbooks to actually generate invoices for rent. Most of the transactions will be mirroring my property account the PM, entering transactions, making sure things reconcile 

I have a 12-unit property and plan to have more in the same company file, so I have followed the advice here and other places and setup classes and sub-classes like this:
- 123 Retirement Blvd
-- Unit 1
-- Unit 2
...

I have also setup Customer, Job, Sub-Job with
- 123 Retirement Blvd
-- Unit 1
--- Jane Renter
-- Unit 2
--- John Tenant
...

So, now I'm going to enter rent from Jane Renter. When entering a transaction for my "PropMgmt Acct" I see that I can tag the transaction with a Customer:Job:SubJob and a Class:SubClass.  Should I be using both? One or the other? Why? 

From your setup, you would need both "job" and "class". I primarily use the "class" function in reports creation in Quickbooks. Then I can generate income statements to do the Schedule E's. Each property has a class code, or more precisely a subcode, corresponding to a property in the Schedule E.

I use the "class" and "subclass" function where "class" is for "state" and subclass is for property. Originally I owned property in more than one state, NY and MA, so I can obtain reports by state.

As to customer and jobs, in your setup, units are associated with customers and jobs with tenants. I primarily own SFR, duplexes and triplexes and had no need to know exactly reports by units, rather by property so I don't set up the tenant as jobs, which is another level down in detail. I simply set them up as customers. Nothing wrong with your setup using jobs, it's little more details than I need.

For data entry purposes, keep your class codes short, or you will have trouble selecting them in the input screens, which has room to show the first six characters. I had to redo my class codes for this reason. 

Using customers and classes offers different reporting options.  I use Classes and Customers for the property address and I use Jobs for the units (if not a single family residence).

I also use classes for each property, but have never seen a reason to break down by unit.  Rather, I have my tenants as customers.  That is very useful, but I don't see the benefit of sub classes for each unit.  Unless you want to generate history for which unit is historically easier to rent, or has a better return.  (a call to your property manager can probably get that info anecdotally.)

When you set up the class codes, if each one starts with a different character, you'll be able to autofill with just one entry letter.  Saves some time.