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ezAccounting can support multiple checking accounts and saving accounts.

How to add a new account
https://www.halfpricesof...counting/add_account.asp 

Please feel free to contact us if you still have any questions.
If you have further questions, please contact us directly at services@halfpricesoft.com
Small business payroll & tax software solution
http://www.halfpricesoft.com 
Hello
I am in the process of evaluating your software as a possible replacement for Quickbooks. I could not find out how to set up multiple checking and savings accounts. We currently have two checking accounts and 4 savings accounts and we need to track deposits and expenses across ledger accounts and into and out of several bank accounts. Can you help me to find this?