But as the properties get larger that smaller percentage = a much larger monthly income than the smaller properties where I have a larger percentage ownership.

I was under the impression that the depreciation percentage depends on the year you are doing the filing.

IRR gives you a percentage that represents the annual return, which can be handy for comparing investments. 

I usually structure my property management payouts by deducting the cleaners' fees from the gross revenue first, then taking my percentage from the remaining balance. 

But even there, the county commissioners are hearing from first-responders that short-term rentals are responsible for a higher percentage of emergency calls -- out-of-staters struggling with altitude, dumb people popping too many edibles and freaking out, etc.

However, they come with the drawbacks of a higher initial investment and potentially lower cash flow percentages.

Quote from @Jacob Zivanovich: I personally don't like percentages when setting aside funds.

Also, you can use "rule of thumb," for lack of better term, percentages but they don't always apply to your local market.

It sounds like you have to do pull the property out all at once, you can't take a percentage.  

Several methods come to mind for the ADU.   1) a regular or periodically adjusted flat fee (based on an estimated usage); 2) factored into the rent (essentially the same as a flat fee); 3) percentage proportionally based on sqft.