Additionally, as the sole person running this business do I need to set it up for my properties to pay the PM company and then the company pays me as an employee or since I'm the owner of the company I don't have any employees and so there would technically be no employee side? 

I set aside more than I normally would for maintenance and repairs because of this. 

Or do you think in 2 years my $200,000 down payment would've just been better in the stock market earning a historical average of 10% (With dividends reinvested, not adjusted for inflation).

Just because you chose to adjust your price doesn't mean it's immediately worth less.

As a option, instead of a commission structure, you can put them on a bonus plan and provide payouts based on a set of criteria. 

The way most people do subject to deals is by setting up a system of checks and balances providing some protection for both buyer and seller, and trying to avoid alerting the lender that a deed transfer has taken place.

If you proceed without any adjustments, the following will be true: - 50% of your potential depreciation recapture will be recognized immediately and become taxable in the year of sale

Feel free to reach out if you ever want to chat about a particular property or you need a second set of eyes to nail down the property you're looking for. 

What apps should I use for setting up a system to invest in tax deeds?

Today's repair costs, eviction costs, set-out costs, and lawyer costs, are more than what 1-2X rent would cover.