How to record owners personal property rent paid through company to him?

Anyone you pay Rent to is a Vendor Name, and that is reportable in Box 1 of a 1099-Misc, most times, as well. Then, they report it as Income to them.

What does "not ran through bank account" have to do with this? How are you Paying them?

The owner has serveral rental properties and he uses tenant cloud as his rental property.  Eight out of the ten belongs to his business property.  He uses tenant cloud to track those two properties along with the eight but only deposits money for the eight into business account and the two he owns personally he deposits those monies into his personal account.

We then transfer basic information into quickbooks for tax purposes since he own serveral other businesses as well. 

Make sure all Rent payments flow to Undeposited Funds. When you select them for deposit, you assign them to a Bank account, or to Owner Draw (Equity).