@Samuel_Gervais perhaps I have misunderstood the question but I would think the bank reconciliation tool will reconcile between the Bank Transactions (loaded by import) and against the corresponding bank account in the Chart of Accounts. At least on other software packages this was how it was happening?
Hence if you have unpaid invoice, there is not yet any entry on the Chart of Accounts’ Bank Account code e.g. 1210. If you pay the invoice then it should show up in the ‘Reconcile the Bank Transaction’ entry.
And the Filters on the window are just used to filter down different types of entries in the Chart of Accounts’ Bank Account e.g. code 1210