Many firms run multiple credit card payments or receive multiple checks to deposit into the bank on the same day. Even though these transactions are run separately, they can be batched together into one amount when they hit the bank account. This process makes it hard to reconcile the firm's bank statement to Zola Suite's individual transactions.
The solution: an Undeposited Funds account per bank account. The Undeposited Funds account will be a temporary holding account for the money to be placed in when you record the payment so that it can be batched and transferred to the appropriate bank account.
Setup:
Create a new Bank Account called "Undeposited Funds: [BankAccount/CreditCardProcessorName]". This can be done for each bank account that will be receiving multiple checks/charges to be deposited. You can also create a single undeposited funds account and post all invoice payments there to later be distributed to the correct bank account.
This account can even mimic your desk drawer or a folder where you may use to hold onto checks until you are ready to go to the bank.
In Banks and Registers, click on the plus sign and select "New Bank Account."
Fill in the details for this account including an Account Name and the Bank Name. Under "Bank Acount Type" select "Undeposited Funds."
Process:
When payments/retainers are made to Zola Suite rather than selecting the actual Bank Account that the check/credit card charge will be deposited to, select the Undeposited Funds Bank Account for that Bank Account. 
Those deposits will accumulate on the register for the undeposited funds account rather than showing as individual deposits in your Operating Account Register.
Those deposits will accumulate on the register for the undeposited funds account rather than showing as individual deposits in your Operating Account Register.
When you are ready to deposit those payments at the banks, Go back to the Banks & Registers and select "Generate Batch Deposit".
Select the undeposited funds account as the "From' account, and the operating Account they are being deposited to as the "To" account. Then select the payments that will be deposited as part of this batch.
This will remove the funds from your undeposited funds account, and show as a total deposit in the Operating account.
If you need to undo the Transfer or part of the transfer, simply delete it by clicking on the trash can icon, or edit it to uncheck specific transactions.
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