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Welcome to the Community, @willanderic! Hope you had a wonderful weekend. :)
Payments can be linked to one bank account at a time, but you can certainly add another bank account and switch when needed. Here's how:
Feel free to view the full article with those steps here: Change the account QuickBooks deposits payments into.
I know our developers would love to hear your suggestion about using different accounts for different card readers. You can leave feedback and suggestions within your QuickBooks account.
Please feel free to reply to this post with any questions. I'm happy to help!