How do you justify on how much to give back on the security deposit if they did not clean up when they left

Yes on lease and it will help you with your mortgage app, make sure you deposit the rental money and document all transactions well for the bank as proof. 

In regards to collecting rent I would just have them continue sending checks (I imagine this is what they were doing); it really does not take much time to deposit a check compared to the training required to teach a possibly technology illiterate person how to; create accounts, link accounts and pay rent.

Number one, as far as I'm aware of, anyone can deposit money into any account- just not take it out. 

She is currently on month to month without any deposit.

So every dollar we deposit is swept directly towards our remaining balance, lowering interest cost and increasing our line available to pull from.

I agree with @Michael Carbonare:  specify the lease terms and the purchase terms.In one deal I did, we agree upon the purchase price, lease amount, and a nonrefundable deposit towards the purchase. 

@Eric BarriosAlways get an estoppel signed by the prior owner an all tenants regarding lease agreement specifics, security deposit held and amount paid or outstanding.There are countless stories of new owner finding out from tenants after the fact a different stories than what was told by the prior owner before the sale.

@Chey ZwickerConfirm verbally that the tenants have been paying on time and then ask for bank statements showing the deposits before accepting the tenants. 

Recently, he mentioned he will be leaving and wanted to see if he could only pay 3200 and I could take off 2 months worth of rent and keep the 500$ deposit .