Start by recording the proper rent payment (in cash) from the tenant. If you use Undeposited Funds, make a deposit to a dummy cash clearing account, then post a payment out from Petty Cash to this Member Draw account. His personal check back to company is Member Contribution or a reverse of the Draw. This is the proper workflow.
Or you could treat his personal check as the tenant payment
The way you suggested to record those transaction look the proper way.
I'm traying to avoid to record a member draw (Latter on on the 1065 Return of Partner Income -schedule K-1, will show that my boss contributed more than the other member). I have separate QB on line for LLC and it won't match. His personal -member draw will be different from contribution on the LLC side.
You also suggested that I could treat his personal check as the tenant payment. I think in this case it will look like he is paying somebody's rent.
Any different idea how to properly record those transaction?