They are closing the gap, and usually offer bill pay, online transfers, mobile deposits, and the other things you would expect.I do highly suggest Amex for business credit cards.

For example, I often see Buyers purchase property thinking there is a $1,000 deposit but then the tenant claims it was $2,000 because they paid the last month's rent.

As an agent representing sellers you should always make sure there is earnest money deposit as part of any accepted offer. 

There is a guy already that removes trash and moves coins around from machines etc, but the seller lives locally when it comes to taking the cash to the bank for deposits. 

Here are the insights from my attorney and CPA:From my attorney:Your approach is perfectly legal and reasonable.From my CPA:Your approach of opening a joint account to pay the mortgage with the deposit coming from the LLC is the correct way.

Then take the cash and deposit to your account. 

Looks like we may be able to make it work using non-QM based on bank deposits.

Handle the deposit like you would at the end of any lease and wish them well. 

Is there any special consideration for taking the security deposit from current manager?

This is advanced rent and is treated similar to a security deposit.