So just figured this out, you can do this by creating sub accounts.

 

First follow this guide to create sub accounts.   I didn’t create any parent accounts, I just created a few sub-accounts under the pre-generated parent account “Checking”.

 

Then add the bank accounts to those sub accounts you created […]

Resolution for 'connect multiple checking accounts from the same bank issue: 'Can I connect multiple checking accounts from the same bank?' available: Yes.

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