But we did not receive the deposit in 24hours.

We have a holding deposit/agreement in place and the lease is already signed and prorated rent paid. 

@Katie Southard For first tenant after we moved who said no way to get to post office during hours, we gave them our keys with signed addendum to the lease that said if they don’t return all of our mailbox keys at lease end, I’m reimbursed for my deposit from their security deposit, and that they are responsible to obtain new keys from post office, themselves, during lease term if lost.

They're fine paying an extra deposit and extra pet fee.

I am looking for advise .We want to move away from security deposits and charge only Move-In Fee.

Let them leave, repair any damages they did (from their deposit) and get it rented to the next tenant after you find out a few things. 

I do not think it only matters whether you were an employee or an independent contractor- I believe most states would look into how the security deposit funds and rental payments are held/ by whom.  

4) Security Deposit Limit: Our tenant has been living at the rental property since 2011.

When the funds have been properly sent, deposited, and received in the account, this document shall become effective.

All in all my contractor quoted repairs around $2k.Am I able to withhold from the security deposit to pay for repairs?