Categorizing Property Management Business Account

I manage the books for a Property Management company. I do have 2 company files - one solely for the company to property track income and expenses and one for the owner to do the same. 

I have hit a snag when it comes to categorizing transactions into the Business Checking account. Since that is the account the owner's income from management fees and reimbursements (for repairs, supplies, etc.) goes into, I want to categorize it as such, but this is where it gets muddled. 

When paying the management fees, I create an expense for each property. When I am entering the transactions for the Business account where the money goes into, should I categorize it as income or something else? The transactions don't match up to the expenses so I am also concerned that I am double-entering them and ultimately making the actual income earned not match.

What is the best way to categorize these transactions in the business file, not the owner's personal one?

Thank you!