You'll need to separate your assets (either by using a Series-LLC or individual LLC with assessed distribution of assets by LLC) and you'll need to separate your passive (asset holding entities) from active operations (the property management side).After you took care of all this you can look into other more complicated/expensive strategies like you describe (equity stripping).Here is a diagram to help you on this quest - talk with @Scott Smith for professional advice on this:

So on one end of the spectrum, I do deals that would be a flat fee type structure I'm assuming, and on the other end I have deals that would operate like a traditional loan but with a balloon.

You're operating under the assumption that the average property sold is equivalent to the average property rented.

Get a strong operating agreement drafted that outlines the purpose of the business and your individual roles in detail.Take it one at a time and grow from there!

Am I protected if I load the properties into an LLC?

I work full time now(40 hrs a week) and own and operate my own plumbing company on the side where I make about 6 times as much.

He did tear out the bathroom as part of the rehab & the stud cavities were loaded with mold but completely removed.

This may be a good solution for you but be sure to understand the law and operate it properly so you don't lose the protections afforded.Most investors I deal with own the property in their own name.

I normally forbid tenants from operating a business from a residential property.

Last year I adopted the Profit First System (Mike Michalowicz) and use the following accounts to manage my business: Operating Expense, Bonus money, Owners Compensation, Tax, and Vacancy/CAPX/Repairs.