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You will need to be a Financial Admin with Full Access to do this.

For teams with split deposits, the chart of accounts (CoAs) for different fees can be connected to different banks. This is why, on the first page of Fees Setup, you see the following note under the Accepted Payment Method(s) section: "*Important: If the chart of accounts used in this registration are connected to different bank accounts (including connected outstanding balances), two credit card transactions will occur."
Accepted Payment Method(s)

The next section, Connect Outstanding Balance, has a Connect Account Outstanding Balance from Billing System setting. When this is set to YES, even if all your CoAs in the registration all send payments to the same bank, it could be CoAs for certain outstanding balances are for the other bank. In this case, the registrant will still see two separate charges to their card, one for CoAs connected to the default bank, and the other for CoAs connected to the secondary bank.
Connect Outstanding Balance

The next setting, Allow Credit Balance to Apply at Checkout?, allows you to apply any credits in the account to their reg total when set to YES. If the credits are greater than the reg cost, the registrant will be charged $0 at checkout; they will not receive a refund.

Note that credits from CoAs connected to one bank will only be applied to charges with CoAs connected to the same bank. For example, suppose they register for the Gold Group for $50 and the CoA "Gold Group Fees" is connected to bank 1. If a $20 credit in their account is for a CoA also connected to bank 1 (regardless of the name), that credit will be applied against the charge and their total will be $30. But if the credit is connected to bank 2, it will not get applied to the charge and so their total will be the full $50.

Once the user proceeds to the checkout for their registration, they will see a notice at the top, "*This registration will appear as two transactions on your credit card invoice," when that is the case.
Registration two transactions notice

Note they will NOT see the transactions listed separately on their registration invoice, but they will see them in both their bank account or credit card provider, and in My Account > Invoices & Payments.
Payments Made This Month

IMPORTANT: When people pay by check and there are CoAs connected to both banks, you will need to enter their check as two separate payments, one for each bank.

See Also
Split deposits and payments by check
Split Deposits - two bank accounts for deposits