I have always utilized multiple accounts for business protection/cash flow management.
The manner in which I have my accounts setup is as follows and involves less risks associated with EFT/Direct Deposit:
My General Business Account functions as my Accounts Receivable account - from which I immediately transfer most of the funds to the business operating account.
My Business Operating Account functions as my Accounts Payable account and that serves the 'main' account.
My Business Savings Account is for gathering funds in preparation for my quarterly estimated Federal and State tax payments that are held in 'reserve' there until the due date approaches, and are then funds are transferred into the Operating Account for issuing these payments.
This method retains all traceability functions and protects the funds in the Accounts Payable portion of my business payments and ensures that there are sufficient funds available for the quarterly estimated Federal and State tax payments.
Good Luck with your decision. 
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