Can I specify a different bank account to deposit Security Deposit and Application Fees to?

Yes, within the particular property record under the Receiving Account field, on the "5. Bank Account" tab, there are two options to select:
"Use different bank account for "Security Deposit"" and "Use different bank account for "Application Fee""

You can select Yes for either option and then select the different bank account to use to deposit to for just those transaction types.
Please note if you are using Master Settings you can set these options on the Bank Account tab.