Need help setting up an SFTP connection for a Financial Institution. Attempting to connect to Scotia Bank SFTP to import bank feeds. Was able to setup the private key, generate the host key, and submit the connectivity configuration, but no Accounts are displayed under Account Linking. Do these need to be added manually? Help documents keep implying it should automatically display a list of accounts to link to GL accounts.

Yes, they need to be set up manually. Depending on the bank, under the Financial Insitution record, you either have a single Format Profile with separate accounts linked under it, or you have multiple Format Profiles, each with a single account linked. Either way, you have to link each account manually.