For the past few months since using them, I've had numerous issues and just as I was about to switch to a different PM company, I was told that the tenants paid only partial rent, and stopped communicating.

If they are using methods #1 or #2 above, their markup is actually built into their pricing!

I'm trying to understand this a bit better, hence the reason for the thread, to weigh in my proposed method versus your proposed method. 

I bought it this year and originally I wanted to do the BRRRR method on it but now I just want to get out from under it.

Is there a better method for someone doing their first deal?

We have had numerous discussions in our group about how to track income and what does that really mean.Recently we had a note that was paid off so in essence it wasn't a sale - or was it?

There are numerous ways to structure it, the most common is a 1-5 year balloon payment where you'll pay them the balance you owe by refinancing with a bank, but you can get as creative as you want with it!  

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I've only gotten a few 4plexes refinanced and it seems they tend to use both comps and the cash flow method.

My first Bigger Pockets book was The Book on Investing in Real Estate with No [and Low] Money Down by Brandon Turner in 2018 and to be honest I was pretty skeptical about some of the methods for owner financing so I decided to keep learning more about real estate investing.