Good Morning! The one thing to do immediately is to update your policy regarding employees living onsite. Half your battle is over, in my opinion, now that the Manager is living offsite.
Employees living onsite should sign a lease and an Employee Housing Agreement that spell out the terms of the Agreement. Usually, in exchange for living onsite rent free, employees cover the property and complete tasks on a weekly and monthly basis. Rent is usually added to the compensation package and taxed accordingly.
When an onsite employee chooses to move offsite and continues working at the property, their compensation is adjusted within a pre-determined time period. Or, your Agreement can specify that salary is re-visited at Annual Review time. Offsite employees may make more once they move offsite, especially if they continue to complete the weekly and monthly tasks (light checks, on-call coverage, etc.)
It is great that the apartment is already updated. Now you can certainly charge more in rent for another resident.
As to the structure of Bonuses: in my opinion you should offer a Bonus per apartment leased. This should not be tied to occupancy. Bonuses tied to occupancy are usually a percentage of overall salary - say 10% of $40,000 would be an annual bonus of $4,000 paid quarterly if all leasing goals are met, etc. I would suggest you create a very structured measureable Bonus Policy so there are objective ways to award employees.
Just because this manager received a "9.1%" salary increase since 2009, does not mean she did not earn it. I think when companies allow employees this type of additional benefit, they must consider the fact that Residents, vendors and other employees interrupt that person to handle emergencies, close pools all summer long, have people knocking on their doors at all hours on some properties and the employee cannot really relax because they are visible at all times and are always representing the company and property. It is not always fun and games living onsite.