When you deposit and withdraw money from your personal bank account, only do it from/to the Holding LLC bank account. 

All I have ran into is paying for marketing, deposit's, etc.

@Hector Ayala, according to this earlier thread, you can (but don't try for a 5-plex or larger):- https://www.biggerpockets.com/forums/432/topics/37...Loan criteria doesn't look too much different from (Non-VA) FHA-Approved Loans, except you might not even have to come up with 3.5% deposit.

It not only saves a lot of hassle, but tenants are never late with direct deposit. 

If they pay rent on time but are not taking good care of the unit, would you keep them then just charge everything through their deposit?

We went in with a $2,000 deposit and offered $27,000 over asking.  

you can google roommate agreements, for a template for ideas.Get a deposit take photo's of interior of each space before renting.

BUT, he also disclosed that apt D only has made a partial deposit of <$100, rent is $600 and on the lease it says this:I suspect he has done this with the other tenants.

No surprises to sellers when 3 days before closing the buyer's tax transcrips haven't come through or their statement shows a cash deposit that can't be accounted for or, surprise, they are on the dead-beat dad list in some state that would have been found out if final approval had taken place before they saw a home.  

I asked for proof of deposits so I know tenants are real and paying real rent, and he said he couldn't provide that because it gets mass deposited with everyone else's rent (he manages 350 units for other people around his town).