@Anonymous
If his living on the property is a condition of his employment, then that value is not income to him.
On the other hand, if he is not required to live on site, then rent is part of his income. Each month you would enter his rent as income, set him up as a customer, and invoice him like any other tenant.
Receive the payment, and deposit it to his mapped 1099 expense account. You may have to deposit it to a cash account first and then make a payment to him in that amount from the cash account.
Journal entries should be the exception when using QB, they often do not work as you think they should, and when you use inventory type items they never work for inventory. It is much better to use the forms on the home page the way QB is designed to be used. Journal entries also bypass reporting, and will not show on many reports.